| Year |
Citation |
Score |
| 2023 |
Tarrés-Solé A, Battistini F, Gerhold JM, Piétrement O, Martínez-García B, Ruiz-López E, Lyonnais S, Bernadó P, Roca J, Orozco M, Le Cam E, Sedman J, Solà M. Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism. Nucleic Acids Research. PMID 37207342 DOI: 10.1093/nar/gkad397 |
0.359 |
|
| 2023 |
Genna V, Iglesias-Fernández J, Reyes-Fraile L, Villegas N, Guckian K, Seth P, Wan B, Cabrero C, Terrazas M, Brun-Heath I, González C, Sciabola S, Villalobos A, Orozco M. Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides. Nucleic Acids Research. PMID 37099382 DOI: 10.1093/nar/gkad309 |
0.331 |
|
| 2023 |
López-Güell K, Battistini F, Orozco M. Correlated motions in DNA: beyond base-pair step models of DNA flexibility. Nucleic Acids Research. PMID 36912082 DOI: 10.1093/nar/gkad136 |
0.339 |
|
| 2023 |
El-Khoury R, Macaluso V, Hennecker C, Mittermaier AK, Orozco M, González C, Garavís M, Damha MJ. i-Motif folding intermediates with zero-nucleotide loops are trapped by 2'-fluoroarabinocytidine via F···H and O···H hydrogen bonds. Communications Chemistry. 6: 31. PMID 36797370 DOI: 10.1038/s42004-023-00831-7 |
0.343 |
|
| 2023 |
Serrano-Chacón I, Mir B, Cupellini L, Colizzi F, Orozco M, Escaja N, González C. pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs. Journal of the American Chemical Society. PMID 36745195 DOI: 10.1021/jacs.2c13043 |
0.644 |
|
| 2023 |
Wieczór M, Tang PK, Orozco M, Cossio P. Omicron mutations increase interdomain interactions and reduce epitope exposure in the SARS-CoV-2 spike. Iscience. 26: 105981. PMID 36694788 DOI: 10.1016/j.isci.2023.105981 |
0.304 |
|
| 2022 |
Suriñach A, Hospital A, Westermaier Y, Jordà L, Orozco-Ruiz S, Beltrán D, Colizzi F, Andrio P, Soliva R, Municoy M, Gelpí JL, Orozco M. High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic Simulations. Journal of Chemical Information and Modeling. PMID 36576351 DOI: 10.1021/acs.jcim.2c01344 |
0.277 |
|
| 2022 |
Paulikat M, Aranda J, Ippoliti E, Orozco M, Carloni P. Proton Transfers to DNA in Native Electrospray Ionization Mass Spectrometry: A Quantum Mechanics/Molecular Mechanics Study. The Journal of Physical Chemistry Letters. 12004-12010. PMID 36540944 DOI: 10.1021/acs.jpclett.2c03100 |
0.358 |
|
| 2022 |
Basu A, Bobrovnikov DG, Cieza B, Arcon JP, Qureshi Z, Orozco M, Ha T. Deciphering the mechanical code of the genome and epigenome. Nature Structural & Molecular Biology. 29: 1178-1187. PMID 36471057 DOI: 10.1038/s41594-022-00877-6 |
0.352 |
|
| 2022 |
Ginex T, Marco-Marín C, Wieczór M, Mata CP, Krieger J, Ruiz-Rodriguez P, López-Redondo ML, Francés-Gómez C, Melero R, Sánchez-Sorzano CÓ, Martínez M, Gougeard N, Forcada-Nadal A, Zamora-Caballero S, Gozalbo-Rovira R, ... ... Orozco M, et al. Correction: The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation. Plos Pathogens. 18: e1010995. PMID 36417341 DOI: 10.1371/journal.ppat.1010995 |
0.226 |
|
| 2022 |
Escobedo A, Piccirillo J, Aranda J, Diercks T, Mateos B, Garcia-Cabau C, Sánchez-Navarro M, Topal B, Biesaga M, Staby L, Kragelund BB, García J, Millet O, Orozco M, Coles M, et al. A glutamine-based single α-helix scaffold to target globular proteins. Nature Communications. 13: 7073. PMID 36400768 DOI: 10.1038/s41467-022-34793-6 |
0.296 |
|
| 2022 |
Ketley RF, Battistini F, Alagia A, Mondielli C, Iehl F, Balikçi E, Huber KVM, Orozco M, Gullerova M. DNA double-strand break-derived RNA drives TIRR/53BP1 complex dissociation. Cell Reports. 41: 111526. PMID 36288694 DOI: 10.1016/j.celrep.2022.111526 |
0.311 |
|
| 2022 |
Neguembor MV, Arcon JP, Buitrago D, Lema R, Walther J, Garate X, Martin L, Romero P, AlHaj Abed J, Gut M, Blanc J, Lakadamyali M, Wu CT, Brun Heath I, Orozco M, et al. MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution. Nature Structural & Molecular Biology. PMID 36220894 DOI: 10.1038/s41594-022-00839-y |
0.29 |
|
| 2022 |
Barissi S, Sala A, Wieczór M, Battistini F, Orozco M. DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors. Nucleic Acids Research. PMID 36018808 DOI: 10.1093/nar/gkac708 |
0.334 |
|
| 2022 |
Wieczór M, Genna V, Aranda J, Badia RM, Gelpí JL, Gapsys V, de Groot BL, Lindahl E, Municoy M, Hospital A, Orozco M. Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. Wiley Interdisciplinary Reviews. Computational Molecular Science. e1622. PMID 35935573 DOI: 10.1002/wcms.1622 |
0.619 |
|
| 2022 |
Ginex T, Marco-Marín C, Wieczór M, Mata CP, Krieger J, Ruiz-Rodriguez P, López-Redondo ML, Francés-Gómez C, Melero R, Sánchez-Sorzano CÓ, Martínez M, Gougeard N, Forcada-Nadal A, Zamora-Caballero S, Gozalbo-Rovira R, ... ... Orozco M, et al. The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation. Plos Pathogens. 18: e1010631. PMID 35816514 DOI: 10.1371/journal.ppat.1010631 |
0.242 |
|
| 2022 |
Bayarri G, Andrio P, Hospital A, Orozco M, Gelpí JL. BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations. Nucleic Acids Research. PMID 35639735 DOI: 10.1093/nar/gkac380 |
0.28 |
|
| 2022 |
Bayarri G, Andrio P, Hospital A, Orozco M, Gelpí JL. BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools. Bioinformatics (Oxford, England). PMID 35543460 DOI: 10.1093/bioinformatics/btac316 |
0.276 |
|
| 2022 |
Aranda J, Wieczór M, Terrazas M, Brun-Heath I, Orozco M. Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2. Chem Catalysis. PMID 35465139 DOI: 10.1016/j.checat.2022.03.019 |
0.267 |
|
| 2022 |
Martin B, Dans PD, Wieczór M, Villegas N, Brun-Heath I, Battistini F, Terrazas M, Orozco M. Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation. Plos Computational Biology. 18: e1009749. PMID 35007284 DOI: 10.1371/journal.pcbi.1009749 |
0.357 |
|
| 2021 |
da Rosa G, Grille L, Calzada V, Ahmad K, Arcon JP, Battistini F, Bayarri G, Bishop T, Carloni P, Cheatham Iii T, Collepardo-Guevara R, Czub J, Espinosa JR, Galindo-Murillo R, Harris SA, ... ... Orozco M, et al. Sequence-dependent structural properties of B-DNA: what have we learned in 40 years? Biophysical Reviews. 13: 995-1005. PMID 35059023 DOI: 10.1007/s12551-021-00893-8 |
0.612 |
|
| 2021 |
Battistini F, Dans PD, Terrazas M, Castellazzi CL, Portella G, Labrador M, Villegas N, Brun-Heath I, González C, Orozco M. The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function. Plos Computational Biology. 17: e1009547. PMID 34748533 DOI: 10.1371/journal.pcbi.1009547 |
0.347 |
|
| 2021 |
Colizzi F, Orozco M. Probing allosteric regulations with coevolution-driven molecular simulations. Science Advances. 7: eabj0786. PMID 34516882 DOI: 10.1126/sciadv.abj0786 |
0.305 |
|
| 2021 |
Bayarri G, Hospital A, Orozco M. 3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories. Frontiers in Molecular Biosciences. 8: 726232. PMID 34485386 DOI: 10.3389/fmolb.2021.726232 |
0.329 |
|
| 2021 |
Buitrago D, Labrador M, Arcon JP, Lema R, Flores O, Esteve-Codina A, Blanc J, Villegas N, Bellido D, Gut M, Dans PD, Heath SC, Gut IG, Brun Heath I, Orozco M. Impact of DNA methylation on 3D genome structure. Nature Communications. 12: 3243. PMID 34050148 DOI: 10.1038/s41467-021-23142-8 |
0.302 |
|
| 2021 |
Bayarri G, Hospital A, Orozco M. 3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories Frontiers in Molecular Biosciences. 8. DOI: 10.3389/fmolb.2021.726232 |
0.329 |
|
| 2020 |
Ribó P, Guo Y, Aranda J, Ainsua-Enrich E, Navinés-Ferrer A, Guerrero M, Pascal M, Cruz C, Orozco M, Muñoz-Cano R, Martin M. MUTATION IN KARS: A NOVEL MECHANISM FOR SEVERE ANAPHYLAXIS. The Journal of Allergy and Clinical Immunology. PMID 33385443 DOI: 10.1016/j.jaci.2020.12.637 |
0.238 |
|
| 2020 |
Moreno D, Zivanovic S, Colizzi F, Hospital A, Aranda J, Soliva R, Orozco M. DFFR: A NEW METHOD FOR HIGH-THROUGHPUT RECALIBRATION OF AUTOMATIC FORCE-FIELDS FOR DRUGS. Journal of Chemical Theory and Computation. PMID 32856910 DOI: 10.1021/acs.jctc.0c00306 |
0.3 |
|
| 2020 |
Zivanovic S, Bayarri G, Colizzi F, Moreno D, Gelpi JL, Soliva R, Hospital A, Orozco M. BIOACTIVE CONFORMATIONAL ENSEMBLE SERVER AND DATABASE. A PUBLIC FRAMEWORK TO SPEED UP IN SILICO DRUG DISCOVERY. Journal of Chemical Theory and Computation. PMID 32786900 DOI: 10.1021/acs.jctc.0c00305 |
0.34 |
|
| 2020 |
Zivanovic S, Colizzi F, Moreno D, Hospital A, Soliva R, Orozco M. EXPLORING THE CONFORMATIONAL LANDSCAPE OF BIOACTIVE SMALL MOLECULES. Journal of Chemical Theory and Computation. PMID 32786895 DOI: 10.1021/acs.jctc.0c00304 |
0.351 |
|
| 2020 |
Wieczór M, Hospital A, Bayarri G, Czub J, Orozco M. Molywood: streamlining the design and rendering of molecular movies. Bioinformatics (Oxford, England). 36: 4660-4661. PMID 32573714 DOI: 10.1093/bioinformatics/btaa584 |
0.3 |
|
| 2020 |
Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, et al. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000research. 9. PMID 32566135 DOI: 10.12688/F1000Research.20559.1 |
0.276 |
|
| 2020 |
Dziubańska-Kusibab PJ, Berger H, Battistini F, Bouwman BAM, Iftekhar A, Katainen R, Cajuso T, Crosetto N, Orozco M, Aaltonen LA, Meyer TF. Colibactin DNA-damage signature indicates mutational impact in colorectal cancer. Nature Medicine. PMID 32483361 DOI: 10.1038/S41591-020-0908-2 |
0.273 |
|
| 2020 |
Sridhar A, Orozco M, Collepardo-Guevara R. Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1. Nucleic Acids Research. PMID 32356891 DOI: 10.1093/Nar/Gkaa285 |
0.288 |
|
| 2020 |
Sati S, Bonev B, Szabo Q, Jost D, Bensadoun P, Serra F, Loubiere V, Papadopoulos GL, Rivera-Mulia JC, Fritsch L, Bouret P, Castillo D, Gelpi JL, Orozco M, Vaillant C, et al. 4D Genome Rewiring during Oncogene-Induced and Replicative Senescence. Molecular Cell. PMID 32220303 DOI: 10.1016/J.Molcel.2020.03.007 |
0.507 |
|
| 2020 |
Sridhar A, Farr SE, Portella G, Schlick T, Orozco M, Collepardo-Guevara R. Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry. Proceedings of the National Academy of Sciences of the United States of America. PMID 32165536 DOI: 10.1073/Pnas.1910044117 |
0.319 |
|
| 2020 |
Walther J, Dans PD, Balaceanu A, Hospital A, Bayarri G, Orozco M. A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level. Nucleic Acids Research. 48: e29. PMID 31956910 DOI: 10.1093/nar/gkaa015 |
0.396 |
|
| 2020 |
Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AM, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, et al. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) F1000research. 9: 278. DOI: 10.12688/f1000research.20559.1 |
0.276 |
|
| 2020 |
Escobedo A, Topal B, Kunze M, Aranda J, Chiesa G, Eftekharzadeh B, Pierattelli R, Felli IC, Diercks T, Millet O, García J, Orozco M, Crehuet R, Lindorff-Larsen K, Salvatella X. Glutamine Side-Chain to Main Chain Hydrogen Bonds Can be used to Design Single Alpha-Helices that are Stable at Room Temperature Biophysical Journal. 118: 369a-370a. DOI: 10.1016/J.Bpj.2019.11.2117 |
0.226 |
|
| 2020 |
Sridhar A, Portella G, Orozco M, Collepardo-Guevara R. Phosphorylation of Intrinsically Disordered Regions within the Genome Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.1680 |
0.194 |
|
| 2019 |
Portella G, Orozco M, Vendruscolo M. Determination of a structural ensemble representing the dynamics of a G-quadruplex DNA. Biochemistry. PMID 31815441 DOI: 10.1021/acs.biochem.9b00493 |
0.399 |
|
| 2019 |
Dans PD, Balaceanu A, Pasi M, Patelli AS, Petkevičiūtė D, Walther J, Hospital A, Bayarri G, Lavery R, Maddocks JH, Orozco M. The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules. Nucleic Acids Research. PMID 31624840 DOI: 10.1093/Nar/Gkz905 |
0.405 |
|
| 2019 |
Andrio P, Hospital A, Conejero J, Jordá L, Del Pino M, Codo L, Soiland-Reyes S, Goble C, Lezzi D, Badia RM, Orozco M, Gelpi JL. BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows. Scientific Data. 6: 169. PMID 31506435 DOI: 10.1038/s41597-019-0177-4 |
0.277 |
|
| 2019 |
Buitrago D, Codó L, Illa R, de Jorge P, Battistini F, Flores O, Bayarri G, Royo R, Del Pino M, Heath S, Hospital A, Gelpí JL, Heath IB, Orozco M. Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning. Nucleic Acids Research. PMID 31504766 DOI: 10.1093/nar/gkz759 |
0.32 |
|
| 2019 |
Janin M, Ortiz-Barahona V, de Moura MC, Martínez-Cardús A, Llinàs-Arias P, Soler M, Nachmani D, Pelletier J, Schumann U, Calleja-Cervantes ME, Moran S, Guil S, Bueno-Costa A, Piñeyro D, Perez-Salvia M, ... ... Orozco M, et al. Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program. Acta Neuropathologica. PMID 31428936 DOI: 10.1007/S00401-019-02062-4 |
0.255 |
|
| 2019 |
Battistini F, Hospital A, Buitrago D, Gallego D, Dans PD, Gelpí JL, Orozco M. How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition. Journal of Molecular Biology. 431: 3845-3859. PMID 31325439 DOI: 10.1016/j.jmb.2019.07.021 |
0.395 |
|
| 2019 |
Gallego D, Darré L, Dans PD, Orozco M. VeriNA3d: an R package for nucleic acids data mining. Bioinformatics (Oxford, England). 35: 5334-5336. PMID 31286135 DOI: 10.1093/bioinformatics/btz553 |
0.292 |
|
| 2019 |
Cuppari A, Fernández-Millán P, Battistini F, Tarrés-Solé A, Lyonnais S, Iruela G, Ruiz-López E, Enciso Y, Rubio-Cosials A, Prohens R, Pons M, Alfonso C, Tóth K, Rivas G, Orozco M, et al. DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region. Nucleic Acids Research. PMID 31114891 DOI: 10.1093/nar/gkz406 |
0.285 |
|
| 2019 |
Hernández-Alvarez MI, Sebastián D, Vives S, Ivanova S, Bartoccioni P, Kakimoto P, Plana N, Veiga SR, Hernández V, Vasconcelos N, Peddinti G, Adrover A, Jové M, Pamplona R, Gordaliza-Alaguero I, ... ... Orozco M, et al. Deficient Endoplasmic Reticulum-Mitochondrial Phosphatidylserine Transfer Causes Liver Disease. Cell. 177: 881-895.e17. PMID 31051106 DOI: 10.1016/j.cell.2019.04.010 |
0.196 |
|
| 2019 |
Escobedo A, Topal B, Kunze MBA, Aranda J, Chiesa G, Mungianu D, Bernardo-Seisdedos G, Eftekharzadeh B, Gairí M, Pierattelli R, Felli IC, Diercks T, Millet O, García J, Orozco M, et al. Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor. Nature Communications. 10: 2034. PMID 31048691 DOI: 10.1038/S41467-019-09923-2 |
0.273 |
|
| 2019 |
Orellana L, Thorne AH, Lema R, Gustavsson J, Parisian AD, Hospital A, Cordeiro TN, Bernadó P, Scott AM, Brun-Heath I, Lindahl E, Cavenee WK, Furnari FB, Orozco M. Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope. Proceedings of the National Academy of Sciences of the United States of America. PMID 31028138 DOI: 10.1073/Pnas.1821442116 |
0.775 |
|
| 2019 |
Arangundy-Franklin S, Taylor AI, Porebski BT, Genna V, Peak-Chew S, Vaisman A, Woodgate R, Orozco M, Holliger P. A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids. Nature Chemistry. PMID 31011171 DOI: 10.1038/s41557-019-0255-4 |
0.295 |
|
| 2019 |
Balaceanu A, Buitrago D, Walther J, Hospital A, Dans PD, Orozco M. Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond. Nucleic Acids Research. 47: 4418-4430. PMID 30957854 DOI: 10.1093/nar/gkz255 |
0.392 |
|
| 2019 |
Colizzi F, Hospital A, Zivanovic S, Orozco M. Predicting the limit of intramolecular H-Bonding with classical molecular dynamics. Angewandte Chemie (International Ed. in English). PMID 30681249 DOI: 10.1002/anie.201810922 |
0.327 |
|
| 2019 |
Terrazas M, Sánchez D, Battistini F, Villegas N, Brun-Heath I, Orozco M. A multifunctional toolkit for target-directed cancer therapy. Chemical Communications (Cambridge, England). 55: 802-805. PMID 30574643 DOI: 10.1039/c8cc08823c |
0.22 |
|
| 2019 |
Orozco M, Luque FJ. Theoretical methods for the description of the solvent effect in biomolecular systems. (Chem. Rev. 2000, 100, 4187-4226. Published on the web oct 21, 2000.). Chemical Reviews. 101: 203-4. PMID 11749364 DOI: 10.1021/CR000703Z |
0.259 |
|
| 2019 |
Orozco M, Luque FJ. Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems. Chemical Reviews. 100: 4187-4226. PMID 11749344 DOI: 10.1021/CR990052A |
0.249 |
|
| 2019 |
Aranda J, Terrazas M, Gómez H, Villegas N, Orozco M. An artificial DNAzyme RNA ligase shows a reaction mechanism resembling that of cellular polymerases Nature Catalysis. 2: 544-552. DOI: 10.1038/s41929-019-0290-y |
0.23 |
|
| 2019 |
Terrazas M, Genna V, Portella G, Villegas N, Sánchez D, Arnan C, Pulido-Quetglas C, Johnson R, Guigó R, Brun-Heath I, Aviñó A, Eritja R, Orozco M. The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry Chem. 5: 1619-1631. DOI: 10.1016/J.CHEMPR.2019.04.002 |
0.234 |
|
| 2019 |
Kuzmanic A, Dans PD, Orozco M. An In-Depth Look at DNA Crystals through the Prism of Molecular Dynamics Simulations Chem. 5: 649-663. DOI: 10.1016/J.CHEMPR.2018.12.007 |
0.354 |
|
| 2019 |
Dans PD, Gallego D, Balaceanu A, Darré L, Gómez H, Orozco M. Modeling, Simulations, and Bioinformatics at the Service of RNA Structure Chem. 5: 51-73. DOI: 10.1016/J.CHEMPR.2018.09.015 |
0.267 |
|
| 2019 |
Sridhar A, Farr S, Portella G, Schlick T, Orozco M, Collepardo-Guevara R. Chromatin Structure Regulation by an Epigenetic Switch Tuning the Flexibility of the H1 C-Terminal Domain Biophysical Journal. 116: 70a. DOI: 10.1016/J.Bpj.2018.11.420 |
0.226 |
|
| 2019 |
Hospital A, Battistini F, Soliva R, Gelpí JL, Orozco M. Surviving the deluge of biosimulation data Wires Computational Molecular Science. 10. DOI: 10.1002/wcms.1449 |
0.186 |
|
| 2018 |
Marti-Renom MA, Almouzni G, Bickmore WA, Bystricky K, Cavalli G, Fraser P, Gasser SM, Giorgetti L, Heard E, Nicodemi M, Nollmann M, Orozco M, Pombo A, Torres-Padilla ME. Challenges and guidelines toward 4D nucleome data and model standards. Nature Genetics. 50: 1352-1358. PMID 30262815 DOI: 10.1038/S41588-018-0236-3 |
0.53 |
|
| 2018 |
Fernández-Zapata J, Pérez-Castaño R, Aranda J, Colizzi F, Polanco MC, Orozco M, Padmanabhan S, Elías-Arnanz M. Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B-based photoreceptor. The Journal of Biological Chemistry. 293: 17888-17905. PMID 30262667 DOI: 10.1074/jbc.RA118.004838 |
0.302 |
|
| 2018 |
Balaceanu A, Pérez A, Dans PD, Orozco M. Allosterism and signal transfer in DNA. Nucleic Acids Research. PMID 29905860 DOI: 10.1093/nar/gky549 |
0.604 |
|
| 2018 |
Garcia-Lopez A, Tessaro F, Jonker HRA, Wacker A, Richter C, Comte A, Berntenis N, Schmucki R, Hatje K, Petermann O, Chiriano G, Perozzo R, Sciarra D, Konieczny P, Faustino I, ... ... Orozco M, et al. Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes. Nature Communications. 9: 2032. PMID 29795225 DOI: 10.1038/S41467-018-04110-1 |
0.297 |
|
| 2018 |
Cunha ES, Sfriso P, Rojas AL, Roversi P, Hospital A, Orozco M, Abrescia NGA. Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop. Structure (London, England : 1993). 26: 181. PMID 29298410 DOI: 10.1016/j.str.2017.11.015 |
0.225 |
|
| 2018 |
Garcia-Lopez A, Wacker A, Tessaro F, Jonker HRA, Richter C, Comte A, Berntenis N, Schmucki R, Hatje K, Sciarra D, Konieczny P, Fournet G, Faustino I, Orozco M, Artero R, et al. NMR solution structure of the TSL2 RNA hairpin Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb5N5C/Pdb |
0.26 |
|
| 2017 |
Rubio-Cosials A, Battistini F, Gansen A, Cuppari A, Bernadó P, Orozco M, Langowski J, Tóth K, Solà M. Protein Flexibility and Synergy of HMG Domains Underlie U-Turn Bending of DNA by TFAM in Solution. Biophysical Journal. PMID 29248151 DOI: 10.1016/J.Bpj.2017.11.3743 |
0.375 |
|
| 2017 |
Mazouzi A, Battistini F, Moser SC, Ferreira da Silva J, Wiedner M, Owusu M, Lardeau CH, Ringler A, Weil B, Neesen J, Orozco M, Kubicek S, Loizou JI. Repair of UV-Induced DNA Damage Independent of Nucleotide Excision Repair Is Masked by MUTYH. Molecular Cell. 68: 797-807.e7. PMID 29149600 DOI: 10.1016/j.molcel.2017.10.021 |
0.285 |
|
| 2017 |
Mir B, Serrano I, Buitrago D, Orozco M, Escaja N, González C. Prevalent sequences in the human genome can form mini i-motif structures at physiological pH. Journal of the American Chemical Society. PMID 28933543 DOI: 10.1021/jacs.7b07383 |
0.304 |
|
| 2017 |
Kotev M, Manuel-Manresa P, Hernando E, Soto-Cerrato V, Orozco M, Quesada R, Perez-Tomas R, Guallar V. Inhibition of Human Enhancer of Zeste Homolog 2 (EZH2) with Tambjamine Analogs. Journal of Chemical Information and Modeling. PMID 28763207 DOI: 10.1021/Acs.Jcim.7B00178 |
0.278 |
|
| 2017 |
Pluta R, Boer DR, Lorenzo-Díaz F, Russi S, Gómez H, Fernández-López C, Pérez-Luque R, Orozco M, Espinosa M, Coll M. Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance. Proceedings of the National Academy of Sciences of the United States of America. PMID 28739894 DOI: 10.1073/pnas.1702971114 |
0.312 |
|
| 2017 |
Porrini M, Rosu F, Rabin C, Darré L, Gómez H, Orozco M, Gabelica V. Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry. Acs Central Science. 3: 454-461. PMID 28573208 DOI: 10.1021/Acscentsci.7B00084 |
0.405 |
|
| 2017 |
López-Ferrando V, Gazzo A, de la Cruz X, Orozco M, Gelpí JL. PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update. Nucleic Acids Research. 45: W222-W228. PMID 28453649 DOI: 10.1093/nar/gkx313 |
0.257 |
|
| 2017 |
Kuzmanic A, Sutto L, Saladino G, Nebreda AR, Gervasio FL, Orozco M. Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations. Elife. 6. PMID 28445123 DOI: 10.7554/eLife.22175 |
0.341 |
|
| 2017 |
Gandioso A, Massaguer A, Villegas N, Salvans C, Sánchez D, Brun-Heath I, Marchán V, Orozco M, Terrazas M. Efficient siRNA-peptide conjugation for specific targeted delivery into tumor cells. Chemical Communications (Cambridge, England). PMID 28218319 DOI: 10.1039/c6cc10287e |
0.211 |
|
| 2017 |
Li J, Lyu W, Rossetti G, Konijnenberg A, Natalello A, Ippoliti E, Orozco M, Sobott F, Grandori R, Carloni P. Proton Dynamics in Protein Mass Spectrometry. The Journal of Physical Chemistry Letters. PMID 28207277 DOI: 10.1021/Acs.Jpclett.7B00127 |
0.326 |
|
| 2017 |
Emperador A, Orozco M. Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins. Journal of Chemical Theory and Computation. 13: 1454-1461. PMID 28157327 DOI: 10.1021/acs.jctc.6b01153 |
0.381 |
|
| 2017 |
Dans PD, Ivani I, Hospital A, Portella G, González C, Orozco M. How accurate are accurate force-fields for B-DNA? Nucleic Acids Research. PMID 28088759 DOI: 10.1093/Nar/Gkw1355 |
0.397 |
|
| 2017 |
Hospital A, Candotti M, Gelpí JL, Orozco M. The Multiple Roles of Waters in Protein Solvation. The Journal of Physical Chemistry. B. 121: 3636-3643. PMID 28059510 DOI: 10.1021/acs.jpcb.6b09676 |
0.333 |
|
| 2017 |
Orellana L, Yoluk Ö, Carrillo O, Orozco M, Lindahl E. Trapping On-Pathway Intermediates for Large Scale Conformational Changes with Coarse-Grained Simulations Biophysical Journal. 112: 485a. DOI: 10.1016/J.Bpj.2016.11.2625 |
0.293 |
|
| 2016 |
Darré L, Ivani I, Dans PD, Gómez H, Hospital A, Orozco M. Small Details Matter: The 2'-Hydroxyl as a Conformational Switch in RNA. Journal of the American Chemical Society. PMID 27957842 DOI: 10.1021/jacs.6b09471 |
0.371 |
|
| 2016 |
Balaceanu A, Pasi M, Dans PD, Hospital A, Lavery R, Orozco M. The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA. The Journal of Physical Chemistry Letters. 21-28. PMID 27935717 DOI: 10.1021/Acs.Jpclett.6B02451 |
0.414 |
|
| 2016 |
Cunha ES, Sfriso P, Rojas AL, Hospital A, Orozco M, Abrescia NG. Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop. Structure (London, England : 1993). PMID 27916518 DOI: 10.1016/J.Str.2016.11.003 |
0.303 |
|
| 2016 |
Chakraborty A, Lyonnais S, Battistini F, Hospital A, Medici G, Prohens R, Orozco M, Vilardell J, Solà M. DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p. Nucleic Acids Research. PMID 27899643 DOI: 10.1093/nar/gkw1147 |
0.371 |
|
| 2016 |
Jaeger S, Igea A, Arroyo R, Alcalde V, Canovas B, Orozco M, Nebreda AR, Aloy P. Quantification of pathway crosstalk reveals novel synergistic drug combinations for breast cancer. Cancer Research. PMID 27879272 DOI: 10.1158/0008-5472.Can-16-0097 |
0.224 |
|
| 2016 |
Orellana L, Yoluk O, Carrillo O, Orozco M, Lindahl E. Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations. Nature Communications. 7: 12575. PMID 27578633 DOI: 10.1038/Ncomms12575 |
0.797 |
|
| 2016 |
Kotev M, Soliva R, Orozco M. Challenges of docking in large, flexible and promiscuous binding sites. Bioorganic & Medicinal Chemistry. PMID 27545443 DOI: 10.1016/j.bmc.2016.08.010 |
0.291 |
|
| 2016 |
Candotti M, Orozco M. The Differential Response of Proteins to Macromolecular Crowding. Plos Computational Biology. 12: e1005040. PMID 27471851 DOI: 10.1371/journal.pcbi.1005040 |
0.328 |
|
| 2016 |
Saint-Léger A, Bello C, Dans PD, Torres AG, Novoa EM, Camacho N, Orozco M, Kondrashov FA, Ribas de Pouplana L. Saturation of recognition elements blocks evolution of new tRNA identities. Science Advances. 2: e1501860. PMID 27386510 DOI: 10.1126/Sciadv.1501860 |
0.248 |
|
| 2016 |
Dans PD, Danilāne L, Ivani I, Dršata T, Lankaš F, Hospital A, Walther J, Pujagut RI, Battistini F, Gelpí JL, Lavery R, Orozco M. Long-timescale dynamics of the Drew-Dickerson dodecamer. Nucleic Acids Research. PMID 27084952 DOI: 10.1093/Nar/Gkw264 |
0.408 |
|
| 2016 |
Hosseini A, Alibés A, Noguera-Julian M, Gil VA, Paredes R, Soliva R, Orozco M, Guallar V. Computational Prediction of HIV-1 Resistance to Protease Inhibitors. Journal of Chemical Information and Modeling. PMID 27082876 DOI: 10.1021/Acs.Jcim.5B00667 |
0.263 |
|
| 2016 |
Orozco M, Srinivasan N. Editorial overview: Theory and simulation. Current Opinion in Structural Biology. 37: iv-v. PMID 27020625 DOI: 10.1016/J.Sbi.2016.03.004 |
0.244 |
|
| 2016 |
Terrazas M, Ivani I, Villegas N, Paris C, Salvans C, Brun-Heath I, Orozco M. Rational design of novel N-alkyl-N capped biostable RNA nanostructures for efficient long-term inhibition of gene expression. Nucleic Acids Research. PMID 26975656 DOI: 10.1093/nar/gkw169 |
0.262 |
|
| 2016 |
Boer DR, Ruiz-Masó JA, Rueda M, Petoukhov MV, Machón C, Svergun DI, Orozco M, Del Solar G, Coll M. Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158. Scientific Reports. 6: 20915. PMID 26875695 DOI: 10.1038/srep20915 |
0.366 |
|
| 2016 |
Deniz Ö, Flores O, Aldea M, Soler-López M, Orozco M. Nucleosome architecture throughout the cell cycle. Scientific Reports. 6: 19729. PMID 26818620 DOI: 10.1038/srep19729 |
0.289 |
|
| 2016 |
Heyn H, Vidal E, Ferreira HJ, Vizoso M, Sayols S, Gomez A, Moran S, Boque-Sastre R, Guil S, Martinez-Cardus A, Lin CY, Royo R, Sanchez-Mut JV, Martinez R, Gut M, ... ... Orozco M, et al. Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer. Genome Biology. 17: 11. PMID 26813288 DOI: 10.1186/S13059-016-0879-2 |
0.276 |
|
| 2016 |
Angarica VE, Orozco M, Sancho J. Exploring the complete mutational space of the LDL receptor LA5 domain using molecular dynamics: linking SNPs with disease phenotypes in familial hypercholesterolemia. Human Molecular Genetics. 25: 1233-46. PMID 26755827 DOI: 10.1093/Hmg/Ddw004 |
0.273 |
|
| 2016 |
Dans PD, Walther J, Gómez H, Orozco M. Multiscale simulation of DNA. Current Opinion in Structural Biology. 37: 29-45. PMID 26708341 DOI: 10.1016/j.sbi.2015.11.011 |
0.349 |
|
| 2016 |
Sfriso P, Duran-Frigola M, Mosca R, Emperador A, Aloy P, Orozco M. Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins. Structure (London, England : 1993). 24: 116-26. PMID 26688214 DOI: 10.1016/J.Str.2015.10.025 |
0.369 |
|
| 2016 |
Shkurti A, Goni R, Andrio P, Breitmoser E, Bethune I, Orozco M, Laughton CA. pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data Softwarex. 5: 44-50. DOI: 10.1016/J.SOFTX.2016.04.002 |
0.318 |
|
| 2016 |
Orellana L, Yoluk O, Orozco M, Lindahl E. Revealing the Mechanism for Conformational Changes from Structurally Rich Ensembles Biophysical Journal. 110: 54a. DOI: 10.1016/J.Bpj.2015.11.358 |
0.36 |
|
| 2015 |
Soteras I, Curutchet C, Bidon-Chanal A, Dehez F, Ángyán JG, Orozco M, Chipot C, Luque FJ. Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations. Journal of Chemical Theory and Computation. 3: 1901-13. PMID 26636193 DOI: 10.1021/ct7001122 |
0.318 |
|
| 2015 |
Emperador A, Meyer T, Orozco M. United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials. Journal of Chemical Theory and Computation. 4: 2001-10. PMID 26620473 DOI: 10.1021/ct8003832 |
0.403 |
|
| 2015 |
Hospital A, Andrio P, Cugnasco C, Codo L, Becerra Y, Dans PD, Battistini F, Torres J, Goñi R, Orozco M, Gelpí JL. BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. Nucleic Acids Research. PMID 26612862 DOI: 10.1093/nar/gkv1301 |
0.374 |
|
| 2015 |
Hospital A, Goñi JR, Orozco M, Gelpí JL. Molecular dynamics simulations: advances and applications. Advances and Applications in Bioinformatics and Chemistry : Aabc. 8: 37-47. PMID 26604800 DOI: 10.2147/AABC.S70333 |
0.389 |
|
| 2015 |
Emperador A, Sfriso P, Villarreal MA, Gelpí JL, Orozco M. PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems. Journal of Chemical Theory and Computation. 11: 5929-38. PMID 26597989 DOI: 10.1021/acs.jctc.5b00660 |
0.372 |
|
| 2015 |
Ivani I, Dans PD, Noy A, Pérez A, Faustino I, Hospital A, Walther J, Andrio P, Goñi R, Balaceanu A, Portella G, Battistini F, Gelpí JL, González C, Vendruscolo M, ... ... Orozco M, et al. Parmbsc1: a refined force field for DNA simulations. Nature Methods. PMID 26569599 DOI: 10.1038/Nmeth.3658 |
0.599 |
|
| 2015 |
Habibian M, Martínez-Montero S, Portella G, Chua Z, Bohle DS, Orozco M, Damha MJ. Seven-Membered Ring Nucleoside Analogues: Stereoselective Synthesis and Studies on Their Conformational Properties. Organic Letters. 17: 5416-9. PMID 26492193 DOI: 10.1021/Acs.Orglett.5B02769 |
0.275 |
|
| 2015 |
Pujol-Pina R, Vilaprinyó-Pascual S, Mazzucato R, Arcella A, Vilaseca M, Orozco M, Carulla N. SDS-PAGE analysis of Aβ oligomers is disserving research into Alzheimer´s disease: appealing for ESI-IM-MS. Scientific Reports. 5: 14809. PMID 26450154 DOI: 10.1038/srep14809 |
0.247 |
|
| 2015 |
Georgieva MV, Yahya G, Codó L, Ortiz R, Teixidó L, Claros J, Jara R, Jara M, Iborra A, Gelpí JL, Gallego C, Orozco M, Aldea M. Inntags: Small self-structured epitopes for innocuous protein tagging Nature Methods. 12: 955-958. PMID 26322837 DOI: 10.1038/nmeth.3556 |
0.28 |
|
| 2015 |
Portella G, Terrazas M, Villegas N, González C, Orozco M. Can A Denaturant Stabilize DNA? Pyridine Reverses DNA Denaturation in Acidic pH. Angewandte Chemie (International Ed. in English). 54: 10488-91. PMID 26224143 DOI: 10.1002/anie.201503770 |
0.355 |
|
| 2015 |
Puente XS, Beà S, Valdés-Mas R, Villamor N, Gutiérrez-Abril J, Martín-Subero JI, Munar M, Rubio-Pérez C, Jares P, Aymerich M, Baumann T, Beekman R, Belver L, Carrio A, Castellano G, ... ... Orozco M, et al. Non-coding recurrent mutations in chronic lymphocytic leukaemia. Nature. PMID 26200345 DOI: 10.1038/Nature14666 |
0.234 |
|
| 2015 |
Collepardo-Guevara R, Portella G, Vendruscolo M, Frenkel D, Schlick T, Orozco M. Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study. Journal of the American Chemical Society. 137: 10205-15. PMID 26192632 DOI: 10.1021/Jacs.5B04086 |
0.315 |
|
| 2015 |
Sáez MA, Fernández-Rodríguez J, Moutinho C, Sanchez-Mut JV, Gomez A, Vidal E, Petazzi P, Szczesna K, Lopez-Serra P, Lucariello M, Lorden P, Delgado-Morales R, de la Caridad OJ, Huertas D, Gelpí JL, ... Orozco M, et al. Mutations in JMJD1C are involved in Rett syndrome and intellectual disability. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 26181491 DOI: 10.1038/Gim.2015.100 |
0.24 |
|
| 2015 |
Rossetti G, Dans PD, Gomez-Pinto I, Ivani I, Gonzalez C, Orozco M. The structural impact of DNA mismatches. Nucleic Acids Research. 43: 4309-21. PMID 25820425 DOI: 10.1093/Nar/Gkv254 |
0.398 |
|
| 2015 |
Barbany M, Meyer T, Hospital A, Faustino I, D'Abramo M, Morata J, Orozco M, de la Cruz X. Molecular dynamics study of naturally existing cavity couplings in proteins. Plos One. 10: e0119978. PMID 25816327 DOI: 10.1371/journal.pone.0119978 |
0.334 |
|
| 2015 |
Martínez-Montero S, Deleavey GF, Dierker-Viik A, Lindovska P, Ilina T, Portella G, Orozco M, Parniak MA, González C, Damha MJ. Synthesis and properties of 2'-deoxy-2',4'-difluoroarabinose-modified nucleic acids. The Journal of Organic Chemistry. 80: 3083-91. PMID 25723361 DOI: 10.1021/Jo502948T |
0.334 |
|
| 2015 |
Gao J, Orozco M, Peishoff CE. Tribute to William L. Jorgensen. The Journal of Physical Chemistry. B. 119: 621-3. PMID 25608798 DOI: 10.1021/Jp511519W |
0.167 |
|
| 2015 |
Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G. Visualizing phosphodiester-bond hydrolysis by an endonuclease. Nature Structural & Molecular Biology. 22: 65-72. PMID 25486305 DOI: 10.1038/nsmb.2932 |
0.312 |
|
| 2015 |
Arcella A, Dreyer J, Ippoliti E, Ivani I, Portella G, Gabelica V, Carloni P, Orozco M. Structure and dynamics of oligonucleotides in the gas phase. Angewandte Chemie (International Ed. in English). 54: 467-71. PMID 25417598 DOI: 10.1002/Anie.201406910 |
0.343 |
|
| 2015 |
Fenollosa C, Otón M, Andrio P, Cortés J, Orozco M, Goñi JR. SEABED: Small molEcule activity scanner weB servicE baseD. Bioinformatics (Oxford, England). 31: 773-5. PMID 25348211 DOI: 10.1093/bioinformatics/btu709 |
0.252 |
|
| 2015 |
Juárez-Jiménez J, Barril X, Orozco M, Pouplana R, Luque FJ. Assessing the suitability of the multilevel strategy for the conformational analysis of small ligands. The Journal of Physical Chemistry. B. 119: 1164-72. PMID 25319869 DOI: 10.1021/jp506779y |
0.349 |
|
| 2015 |
Emperador A, Sfriso P, Villarreal MA, Gelpí JL, Orozco M. PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems Journal of Chemical Theory and Computation. 11: 5929-5938. DOI: 10.1021/acs.jctc.5b00660 |
0.372 |
|
| 2015 |
Arcella A, Dreyer J, Ippoliti E, Ivani I, Portella G, Gabelica V, Carloni P, Orozco M. Structure and dynamics of oligonucleotides in the gas phase Angewandte Chemie - International Edition. 54: 467-471. DOI: 10.1002/anie.201406910 |
0.274 |
|
| 2014 |
Moncunill V, Gonzalez S, Beà S, Andrieux LO, Salaverria I, Royo C, Martinez L, Puiggròs M, Segura-Wang M, Stütz AM, Navarro A, Royo R, Gelpí JL, Gut IG, López-Otín C, ... Orozco M, et al. Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads. Nature Biotechnology. 32: 1106-12. PMID 25344728 DOI: 10.1038/Nbt.3027 |
0.264 |
|
| 2014 |
Pasi M, Maddocks JH, Beveridge D, Bishop TC, Case DA, Cheatham T, Dans PD, Jayaram B, Lankas F, Laughton C, Mitchell J, Osman R, Orozco M, Pérez A, Petkevi?i?t? D, et al. μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Research. 42: 12272-83. PMID 25260586 DOI: 10.1093/Nar/Gku855 |
0.616 |
|
| 2014 |
Dans PD, Faustino I, Battistini F, Zakrzewska K, Lavery R, Orozco M. Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA. Nucleic Acids Research. 42: 11304-20. PMID 25223784 DOI: 10.1093/Nar/Gku809 |
0.315 |
|
| 2014 |
Cuervo A, Dans PD, Carrascosa JL, Orozco M, Gomila G, Fumagalli L. Direct measurement of the dielectric polarization properties of DNA. Proceedings of the National Academy of Sciences of the United States of America. 111: E3624-30. PMID 25136104 DOI: 10.1073/Pnas.1405702111 |
0.389 |
|
| 2014 |
Carmona FJ, Davalos V, Vidal E, Gomez A, Heyn H, Hashimoto Y, Vizoso M, Martinez-Cardus A, Sayols S, Ferreira HJ, Sánchez-Mut JV, Morán S, Margelí M, Castella E, Berdasco M, ... ... Orozco M, et al. A comprehensive DNA methylation profile of epithelial-to-mesenchymal transition. Cancer Research. 74: 5608-19. PMID 25106427 DOI: 10.1158/0008-5472.Can-13-3659 |
0.284 |
|
| 2014 |
Arcella A, Portella G, Collepardo-Guevara R, Chakraborty D, Wales DJ, Orozco M. Structure and properties of DNA in apolar solvents. The Journal of Physical Chemistry. B. 118: 8540-8. PMID 24968001 DOI: 10.1021/Jp503816R |
0.356 |
|
| 2014 |
Fenwick RB, Orellana L, Esteban-Martín S, Orozco M, Salvatella X. Correlated motions are a fundamental property of β-sheets. Nature Communications. 5: 4070. PMID 24915882 DOI: 10.1038/ncomms5070 |
0.73 |
|
| 2014 |
Orozco M. A theoretical view of protein dynamics. Chemical Society Reviews. 43: 5051-66. PMID 24709805 DOI: 10.1039/c3cs60474h |
0.354 |
|
| 2014 |
Flores O, Deniz Ö, Soler-López M, Orozco M. Fuzziness and noise in nucleosomal architecture. Nucleic Acids Research. 42: 4934-46. PMID 24586063 DOI: 10.1093/nar/gku165 |
0.258 |
|
| 2014 |
Portella G, Germann MW, Hud NV, Orozco M. MD and NMR analyses of choline and TMA binding to duplex DNA: on the origins of aberrant sequence-dependent stability by alkyl cations in aqueous and water-free solvents. Journal of the American Chemical Society. 136: 3075-86. PMID 24490755 DOI: 10.1021/Ja410698U |
0.361 |
|
| 2014 |
Aviñó A, Portella G, Ferreira R, Gargallo R, Mazzini S, Gabelica V, Orozco M, Eritja R. Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures Febs Journal. 281: 1085-1099. PMID 24304855 DOI: 10.1111/Febs.12670 |
0.335 |
|
| 2014 |
Faustino I, Curutchet C, Luque FJ, Orozco M. The DNA-forming properties of 6-selenoguanine. Physical Chemistry Chemical Physics : Pccp. 16: 1101-10. PMID 24287926 DOI: 10.1039/c3cp53885k |
0.379 |
|
| 2013 |
Jamroz M, Orozco M, Kolinski A, Kmiecik S. Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field. Journal of Chemical Theory and Computation. 9: 119-25. PMID 26589015 DOI: 10.1021/ct300854w |
0.386 |
|
| 2013 |
Emperador A, Solernou A, Sfriso P, Pons C, Gelpi JL, Fernandez-Recio J, Orozco M. Efficient Relaxation of Protein-Protein Interfaces by Discrete Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 9: 1222-9. PMID 26588765 DOI: 10.1021/ct301039e |
0.641 |
|
| 2013 |
Candotti M, Pérez A, Ferrer-Costa C, Rueda M, Meyer T, Gelpà JL, Orozco M. Exploring early stages of the chemical unfolding of proteins at the proteome scale. Plos Computational Biology. 9: e1003393. PMID 24348236 DOI: 10.1371/journal.pcbi.1003393 |
0.365 |
|
| 2013 |
Rueda M, Orozco M, Totrov M, Abagyan R. BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry. Bmc Structural Biology. 13: 32. PMID 24330655 DOI: 10.1186/1472-6807-13-32 |
0.278 |
|
| 2013 |
Portella G, Battistini F, Orozco M. Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations. Plos Computational Biology. 9: e1003354. PMID 24278005 DOI: 10.1371/journal.pcbi.1003354 |
0.319 |
|
| 2013 |
Naganathan AN, Orozco M. The conformational landscape of an intrinsically disordered DNA-binding domain of a transcription regulator. The Journal of Physical Chemistry. B. 117: 13842-50. PMID 24127726 DOI: 10.1021/Jp408350V |
0.383 |
|
| 2013 |
Martin-Pintado N, Deleavey GF, Portella G, Campos-Olivas R, Orozco M, Damha MJ, González C. Backbone FC-H···O hydrogen bonds in 2'F-substituted nucleic acids. Angewandte Chemie (International Ed. in English). 52: 12065-8. PMID 24115468 DOI: 10.1002/Anie.201305710 |
0.329 |
|
| 2013 |
Dršata T, Pérez A, Orozco M, Morozov AV, Sponer J, Lankaš F. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. Journal of Chemical Theory and Computation. 9: 707-721. PMID 23976886 DOI: 10.1021/Ct300671Y |
0.65 |
|
| 2013 |
D'Abramo M, Castellazzi CL, Orozco M, Amadei A. On the nature of DNA hyperchromic effect. The Journal of Physical Chemistry. B. 117: 8697-704. PMID 23799235 DOI: 10.1021/jp403369k |
0.363 |
|
| 2013 |
Durán E, Djebali S, González S, Flores O, Mercader JM, Guigó R, Torrents D, Soler-López M, Orozco M. Unravelling the hidden DNA structural/physical code provides novel insights on promoter location. Nucleic Acids Research. 41: 7220-30. PMID 23761436 DOI: 10.1093/nar/gkt511 |
0.319 |
|
| 2013 |
Sfriso P, Hospital A, Emperador A, Orozco M. Exploration of conformational transition pathways from coarse-grained simulations. Bioinformatics (Oxford, England). 29: 1980-6. PMID 23740746 DOI: 10.1093/bioinformatics/btt324 |
0.38 |
|
| 2013 |
Hospital A, Faustino I, Collepardo-Guevara R, González C, Gelpí JL, Orozco M. NAFlex: a web server for the study of nucleic acid flexibility. Nucleic Acids Research. 41: W47-55. PMID 23685436 DOI: 10.1093/Nar/Gkt378 |
0.394 |
|
| 2013 |
Candotti M, Esteban-Martín S, Salvatella X, Orozco M. Toward an atomistic description of the urea-denatured state of proteins. Proceedings of the National Academy of Sciences of the United States of America. 110: 5933-8. PMID 23536295 DOI: 10.1073/pnas.1216589110 |
0.343 |
|
| 2013 |
Martín-Pintado N, Yahyaee-Anzahaee M, Deleavey GF, Portella G, Orozco M, Damha MJ, González C. Dramatic effect of furanose C2' substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom. Journal of the American Chemical Society. 135: 5344-7. PMID 23521511 DOI: 10.1021/Ja401954T |
0.293 |
|
| 2013 |
Terrazas M, Alagia A, Faustino I, Orozco M, Eritja R. Functionalization of the 3'-ends of DNA and RNA strands with N-ethyl-N-coupled nucleosides: a promising approach to avoid 3'-exonuclease-catalyzed hydrolysis of therapeutic oligonucleotides. Chembiochem : a European Journal of Chemical Biology. 14: 510-20. PMID 23362010 DOI: 10.1002/cbic.201200611 |
0.311 |
|
| 2013 |
Islam B, Sgobba M, Laughton C, Orozco M, Sponer J, Neidle S, Haider S. Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale Nucleic Acids Research. 41: 2723-2735. PMID 23293000 DOI: 10.1093/Nar/Gks1331 |
0.415 |
|
| 2013 |
Sciabola S, Cao Q, Orozco M, Faustino I, Stanton RV. Improved nucleic acid descriptors for siRNA efficacy prediction. Nucleic Acids Research. 41: 1383-94. PMID 23241392 DOI: 10.1093/nar/gks1191 |
0.325 |
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| 2013 |
Gracia E, Farré D, Cortés A, Ferrer-Costa C, Orozco M, Mallol J, Lluís C, Canela EI, McCormick PJ, Franco R, Fanelli F, Casadó V. The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 27: 1048-61. PMID 23193172 DOI: 10.1096/Fj.12-212621 |
0.494 |
|
| 2013 |
Orozco M. The dynamic view of proteins: comment on "Comparing proteins to their internal dynamics: exploring structure-function relationships beyond static structural alignments". Physics of Life Reviews. 10: 29-30; discussion 39. PMID 23154221 DOI: 10.1016/j.plrev.2012.10.010 |
0.342 |
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| 2013 |
Raimondi F, Felline A, Portella G, Orozco M, Fanelli F. Light on the structural communication in Ras GTPases. Journal of Biomolecular Structure & Dynamics. 31: 142-57. PMID 22849539 DOI: 10.1080/07391102.2012.698379 |
0.27 |
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| 2013 |
Martin-Pintado N, Yahyaee-Anzahaee M, Deleavey GF, Portella G, Orozco M, Damha MJ, Gonzalez C. Parallel human telomeric quadruplex containing 2'F-ANA substitutions Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2M1G/Pdb |
0.204 |
|
| 2013 |
Meyer T, Gabelica V, Grubmüller H, Orozco M. Proteins in the gas phase Wiley Interdisciplinary Reviews: Computational Molecular Science. 3: 408-425. DOI: 10.1002/Wcms.1130 |
0.313 |
|
| 2013 |
Orozco M. Innovations in Biomolecular Modeling and Simulations. Edited by Tamar Schlick Chemmedchem. 8: 1012-1014. DOI: 10.1002/cmdc.201300052 |
0.271 |
|
| 2012 |
Sfriso P, Emperador A, Orellana L, Hospital A, Gelpí JL, Orozco M. Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 8: 4707-18. PMID 26605625 DOI: 10.1021/ct300494q |
0.757 |
|
| 2012 |
Forti F, Cavasotto CN, Orozco M, Barril X, Luque FJ. A Multilevel Strategy for the Exploration of the Conformational Flexibility of Small Molecules. Journal of Chemical Theory and Computation. 8: 1808-19. PMID 26593672 DOI: 10.1021/ct300097s |
0.335 |
|
| 2012 |
Carrillo O, Laughton CA, Orozco M. Fast Atomistic Molecular Dynamics Simulations from Essential Dynamics Samplings. Journal of Chemical Theory and Computation. 8: 792-9. PMID 26593340 DOI: 10.1021/ct2007296 |
0.393 |
|
| 2012 |
Chaudhuri R, Carrillo O, Laughton CA, Orozco M. Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design. Journal of Chemical Theory and Computation. 8: 2204-14. PMID 26588953 DOI: 10.1021/ct300223c |
0.379 |
|
| 2012 |
Nadal-Ribelles M, Conde N, Flores O, González-Vallinas J, Eyras E, Orozco M, de Nadal E, Posas F. Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling. Genome Biology. 13: R106. PMID 23158682 DOI: 10.1186/gb-2012-13-11-r106 |
0.208 |
|
| 2012 |
Kulis M, Heath S, Bibikova M, Queirós AC, Navarro A, Clot G, MartÃnez-Trillos A, Castellano G, Brun-Heath I, Pinyol M, Barberán-Soler S, Papasaikas P, Jares P, Beà S, Rico D, ... ... Orozco M, et al. Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nature Genetics. 44: 1236-42. PMID 23064414 DOI: 10.1038/Ng.2443 |
0.3 |
|
| 2012 |
Dans PD, Pérez A, Faustino I, Lavery R, Orozco M. Exploring polymorphisms in B-DNA helical conformations. Nucleic Acids Research. 40: 10668-78. PMID 23012264 DOI: 10.1093/nar/gks884 |
0.63 |
|
| 2012 |
García-Fandiño R, Bernadó P, Ayuso-Tejedor S, Sancho J, Orozco M. Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case. Plos Computational Biology. 8: e1002647. PMID 22927805 DOI: 10.1371/Journal.Pcbi.1002647 |
0.346 |
|
| 2012 |
Pérez A, Castellazzi CL, Battistini F, Collinet K, Flores O, Deniz O, Ruiz ML, Torrents D, Eritja R, Soler-López M, Orozco M. Impact of methylation on the physical properties of DNA. Biophysical Journal. 102: 2140-8. PMID 22824278 DOI: 10.1016/j.bpj.2012.03.056 |
0.305 |
|
| 2012 |
Barbany M, Morata J, Meyer T, Lois S, Orozco M, de la Cruz X. Characterization of the impact of alternative splicing on protein dynamics: the cases of glutathione S-transferase and ectodysplasin-A isoforms. Proteins. 80: 2235-49. PMID 22576332 DOI: 10.1002/prot.24112 |
0.356 |
|
| 2012 |
Hospital A, Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelpí JL. MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics (Oxford, England). 28: 1278-9. PMID 22437851 DOI: 10.1093/bioinformatics/bts139 |
0.332 |
|
| 2012 |
Arcella A, Portella G, Ruiz ML, Eritja R, Vilaseca M, Gabelica V, Orozco M. Structure of triplex DNA in the Gas phase Journal of the American Chemical Society. 134: 6596-6606. PMID 22420643 DOI: 10.1021/Ja209786T |
0.38 |
|
| 2012 |
Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, ... ... Orozco M, et al. Evidence for transcript networks composed of chimeric RNAs in human cells. Plos One. 7: e28213. PMID 22238572 DOI: 10.1371/Journal.Pone.0028213 |
0.234 |
|
| 2012 |
Quesada V, Conde L, Villamor N, Ordóñez GR, Jares P, Bassaganyas L, Ramsay AJ, Beà S, Pinyol M, MartÃnez-Trillos A, López-Guerra M, Colomer D, Navarro A, Baumann T, Aymerich M, ... ... Orozco M, et al. Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nature Genetics. 44: 47-52. PMID 22158541 DOI: 10.1038/Ng.1032 |
0.239 |
|
| 2012 |
Pérez A, Luque FJ, Orozco M. Frontiers in molecular dynamics simulations of DNA. Accounts of Chemical Research. 45: 196-205. PMID 21830782 DOI: 10.1021/ar2001217 |
0.638 |
|
| 2012 |
Utz N, Meyer T, Rink G, Orozco M, Koslowski T. Geometry, Dynamics, and Electronic Structure of DNA–Carbon Nanotube Hybrids The Journal of Physical Chemistry C. 116: 11278-11282. DOI: 10.1021/JP210232S |
0.283 |
|
| 2011 |
Deniz O, Flores O, Battistini F, Pérez A, Soler-López M, Orozco M. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. Bmc Genomics. 12: 489. PMID 21981773 DOI: 10.1186/1471-2164-12-489 |
0.58 |
|
| 2011 |
Orozco M, Orellana L, Hospital A, Naganathan AN, Emperador A, Carrillo O, Gelpí JL. Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings. Advances in Protein Chemistry and Structural Biology. 85: 183-215. PMID 21920324 DOI: 10.1016/B978-0-12-386485-7.00005-3 |
0.742 |
|
| 2011 |
Blas JR, Huertas O, Tabares C, Sumpter BG, Fuentes-Cabrera M, Orozco M, Ordejón P, Luque FJ. Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases. The Journal of Physical Chemistry. A. 115: 11344-54. PMID 21888322 DOI: 10.1021/jp205122c |
0.395 |
|
| 2011 |
Naganathan AN, Orozco M. The protein folding transition-state ensemble from a Gō-like model. Physical Chemistry Chemical Physics : Pccp. 13: 15166-74. PMID 21776506 DOI: 10.1039/C1Cp20964G |
0.33 |
|
| 2011 |
Naganathan AN, Orozco M. The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding. Journal of the American Chemical Society. 133: 12154-61. PMID 21732676 DOI: 10.1021/Ja204053N |
0.39 |
|
| 2011 |
Flores O, Orozco M. nucleR: a package for non-parametric nucleosome positioning. Bioinformatics (Oxford, England). 27: 2149-50. PMID 21653521 DOI: 10.1093/bioinformatics/btr345 |
0.233 |
|
| 2011 |
Stein A, Rueda M, Panjkovich A, Orozco M, Aloy P. A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks. Structure (London, England : 1993). 19: 881-9. PMID 21645858 DOI: 10.1016/J.Str.2011.03.009 |
0.343 |
|
| 2011 |
Puente XS, Pinyol M, Quesada V, Conde L, Ordóñez GR, Villamor N, Escaramis G, Jares P, Beà S, González-Díaz M, Bassaganyas L, Baumann T, Juan M, López-Guerra M, Colomer D, ... ... Orozco M, et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature. 475: 101-5. PMID 21642962 DOI: 10.1038/Nature10113 |
0.239 |
|
| 2011 |
Raimondi F, Portella G, Orozco M, Fanelli F. Nucleotide binding switches the information flow in ras GTPases. Plos Computational Biology. 7: e1001098. PMID 21390270 DOI: 10.1371/journal.pcbi.1001098 |
0.325 |
|
| 2011 |
Kowalczyk L, Ratera M, Paladino A, Bartoccioni P, Errasti-Murugarren E, Valencia E, Portella G, Bial S, Zorzano A, Fita I, Orozco M, Carpena X, Vázquez-Ibar JL, Palacín M. Molecular basis of substrate-induced permeation by an amino acid antiporter. Proceedings of the National Academy of Sciences of the United States of America. 108: 3935-40. PMID 21368142 DOI: 10.1073/pnas.1018081108 |
0.294 |
|
| 2011 |
Ayuso-Tejedor S, García-Fandiño R, Orozco M, Sancho J, Bernadó P. Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering. Journal of Molecular Biology. 406: 604-19. PMID 21216251 DOI: 10.1016/J.Jmb.2010.12.027 |
0.349 |
|
| 2011 |
Pons C, Talavera D, de la Cruz X, Orozco M, Fernandez-Recio J. Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking. Journal of Chemical Information and Modeling. 51: 370-7. PMID 21214199 DOI: 10.1021/Ci100353E |
0.617 |
|
| 2011 |
Portella G, Orozco M. Multiple routes to characterize the folding of a small DNA hairpin. Angewandte Chemie (International Ed. in English). 49: 7673-6. PMID 20845348 DOI: 10.1002/anie.201003816 |
0.319 |
|
| 2011 |
Palacín M, Kowalczyk L, Ratera M, Paladino A, Bartoccioni P, Errasti E, Valencia E, Portella G, Bial S, Zorzano A, Fita I, Orozco M, Carpena X, Vázquez-Ibar JL. Molecular basis of substrate-induced permeation by an amino acid antiporter Acta Crystallographica Section a Foundations of Crystallography. 67: C186-C186. DOI: 10.1107/S0108767311095353 |
0.264 |
|
| 2011 |
Luque FJ, Dehez F, Chipot C, Orozco M. Polarization effects in molecular interactions Wires Computational Molecular Science. 1: 844-854. DOI: 10.1002/wcms.32 |
0.27 |
|
| 2010 |
Banáš P, Hollas D, Zgarbová M, Jurečka P, Orozco M, Cheatham TE, Šponer J, Otyepka M. Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins. Journal of Chemical Theory and Computation. 6: 3836-3849. PMID 35283696 DOI: 10.1021/ct100481h |
0.33 |
|
| 2010 |
Orellana L, Rueda M, Ferrer-Costa C, Lopez-Blanco JR, Chacón P, Orozco M. Approaching Elastic Network Models to Molecular Dynamics Flexibility. Journal of Chemical Theory and Computation. 6: 2910-23. PMID 26616090 DOI: 10.1021/Ct100208E |
0.755 |
|
| 2010 |
Novoa EM, Ribas de Pouplana L, Barril X, Orozco M. Ensemble Docking from Homology Models. Journal of Chemical Theory and Computation. 6: 2547-57. PMID 26613506 DOI: 10.1021/Ct100246Y |
0.32 |
|
| 2010 |
D'Abramo M, Orozco M, Amadei A. Effects of local electric fields on the redox free energy of single stranded DNA. Chemical Communications (Cambridge, England). 47: 2646-8. PMID 21180762 DOI: 10.1039/c0cc04352d |
0.311 |
|
| 2010 |
Meyer T, D'Abramo M, Hospital A, Rueda M, Ferrer-Costa C, Pérez A, Carrillo O, Camps J, Fenollosa C, Repchevsky D, Gelpí JL, Orozco M. MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories. Structure (London, England : 1993). 18: 1399-409. PMID 21070939 DOI: 10.1016/j.str.2010.07.013 |
0.625 |
|
| 2010 |
Faustino I, Pérez A, Orozco M. Toward a consensus view of duplex RNA flexibility. Biophysical Journal. 99: 1876-85. PMID 20858433 DOI: 10.1016/j.bpj.2010.06.061 |
0.588 |
|
| 2010 |
Pons C, D'Abramo M, Svergun DI, Orozco M, Bernadó P, Fernández-Recio J. Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data. Journal of Molecular Biology. 403: 217-30. PMID 20804770 DOI: 10.1016/J.Jmb.2010.08.029 |
0.609 |
|
| 2010 |
Aviñó A, Cubero E, Gargallo R, González C, Orozco M, Eritja R. Structural properties of g,t-parallel duplexes. Journal of Nucleic Acids. 2010. PMID 20798879 DOI: 10.4061/2010/763658 |
0.361 |
|
| 2010 |
Perez A, Orozco M. Real-time atomistic description of DNA unfolding. Angewandte Chemie (International Ed. in English). 49: 4805-8. PMID 20480472 DOI: 10.1002/anie.201000593 |
0.569 |
|
| 2010 |
Soteras I, Orozco M, Luque FJ. Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies. Journal of Computer-Aided Molecular Design. 24: 281-91. PMID 20300801 DOI: 10.1007/s10822-010-9331-y |
0.288 |
|
| 2010 |
Raimondi F, Orozco M, Fanelli F. Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily. Structure (London, England : 1993). 18: 402-14. PMID 20223222 DOI: 10.1016/j.str.2009.12.015 |
0.262 |
|
| 2010 |
Watts JK, Martín-Pintado N, Gómez-Pinto I, Schwartzentruber J, Portella G, Orozco M, González C, Damha MJ. Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility. Nucleic Acids Research. 38: 2498-511. PMID 20071751 DOI: 10.1093/Nar/Gkp1225 |
0.268 |
|
| 2010 |
Novoa EM, Castro de Moura M, Orozco M, Ribas de Pouplana L. A genomics method to identify pathogenicity-related proteins. Application to aminoacyl-tRNA synthetase-like proteins. Febs Letters. 584: 460-6. PMID 19913539 DOI: 10.1016/J.Febslet.2009.11.016 |
0.275 |
|
| 2010 |
García-Fandiño R, Granja JR, D'Abramo M, Orozco M. Theoretical characterization of the dynamical behavior and transport properties of alpha,gamma-peptide nanotubes in solution. Journal of the American Chemical Society. 131: 15678-86. PMID 19860480 DOI: 10.1021/ja903400n |
0.35 |
|
| 2010 |
Lavery R, Zakrzewska K, Beveridge D, Bishop TC, Case DA, Cheatham T, Dixit S, Jayaram B, Lankas F, Laughton C, Maddocks JH, Michon A, Osman R, Orozco M, Perez A, et al. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Research. 38: 299-313. PMID 19850719 DOI: 10.1093/Nar/Gkp834 |
0.638 |
|
| 2010 |
Emperador A, Meyer T, Orozco M. Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials. Proteins. 78: 83-94. PMID 19816993 DOI: 10.1002/prot.22563 |
0.398 |
|
| 2010 |
Banáš P, Hollas D, Zgarbová M, Jurečka P, Orozco M, Cheatham TE, Šponer J, Otyepka M. Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins Journal of Chemical Theory and Computation. 6: 3836-3849. DOI: 10.1021/Ct100481H |
0.325 |
|
| 2010 |
Lavilla R, Coll O, Bosch J, Orozco M, Luque FJ. ChemInform Abstract: General Access to Tacamine and Vinca-Eburna Alkaloids Through Tandem Non-Biomimetic Oxidation of Dihydropyridines/Zn-Mediated Radical Addition Processes - Unexpected Facial Selectivity of Flattened Cyclohexyl-Type Radicals. Cheminform. 33: no-no. DOI: 10.1002/CHIN.200217211 |
0.21 |
|
| 2010 |
Amat M, Bosch J, Hidalgo J, Canto M, Perez M, Llor N, Molins E, Miravitlles C, Orozco M, Luque J. ChemInform Abstract: Synthesis of Enantiopure trans-3,4-Disubstituted Piperidines. An Enantiodivergent Synthesis of (+)- and (-)-Paroxetine. Cheminform. 31: no-no. DOI: 10.1002/CHIN.200035122 |
0.198 |
|
| 2010 |
BASTIDA J, CODINA C, PEETERS P, RUBIRALTA M, OROZCO M, LUQUE FJ, CHHABRA SC. ChemInform Abstract: Alkaloids from Crinum kirkii. Cheminform. 27: no-no. DOI: 10.1002/CHIN.199610275 |
0.197 |
|
| 2010 |
MIGUEL D, DIEZ A, BLACHE Y, LUQUE J, OROZCO M, REMUSON R, GELAS-MIALHE Y, RUBIRALTA M. ChemInform Abstract: Synthetic Studies on Indole Alkaloids. Part 8. Synthesis and Reactivity of Asymmetric 2-Indolyl-4-methylenepiperidines. Cheminform. 26: no-no. DOI: 10.1002/CHIN.199543178 |
0.213 |
|
| 2010 |
OROZCO M, ALEMAN C, LUQUE FJ. ChemInform Abstract: Force Field Parametrization from Quantum Mechanical Data Cheminform. 25: no-no. DOI: 10.1002/CHIN.199403303 |
0.236 |
|
| 2009 |
Fadrná E, Špačková N, Sarzyñska J, Koča J, Orozco M, Cheatham TE, Kulinski T, Šponer J. Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields. Journal of Chemical Theory and Computation. 5: 2514-30. PMID 26616629 DOI: 10.1021/Ct900200K |
0.403 |
|
| 2009 |
D'Abramo M, Meyer T, Bernadó P, Pons C, Recio JF, Orozco M. On the Use of low-resolution Data to Improve Structure Prediction of Proteins and Protein Complexes. Journal of Chemical Theory and Computation. 5: 3129-37. PMID 26609992 DOI: 10.1021/Ct900305M |
0.303 |
|
| 2009 |
Xie W, Orozco M, Truhlar DG, Gao J. X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water. Journal of Chemical Theory and Computation. 5: 459-467. PMID 20490369 DOI: 10.1021/Ct800239Q |
0.341 |
|
| 2009 |
Noy A, Soteras I, Luque FJ, Orozco M. The impact of monovalent ion force field model in nucleic acids simulations. Physical Chemistry Chemical Physics : Pccp. 11: 10596-607. PMID 20145804 DOI: 10.1039/b912067j |
0.353 |
|
| 2009 |
Laughton CA, Orozco M. Nucleic acid simulations themed issue. Physical Chemistry Chemical Physics : Pccp. 11: 10541-2. PMID 20145799 DOI: 10.1039/b921472k |
0.271 |
|
| 2009 |
Vázquez-Mayagoitia A, Huertas O, Brancolini G, Migliore A, Sumpter BG, Orozco M, Luque FJ, Di Felice R, Fuentes-Cabrera M. Ab initio study of the structural, tautomeric, pairing, and electronic properties of seleno-derivatives of thymine. The Journal of Physical Chemistry. B. 113: 14465-72. PMID 19813710 DOI: 10.1021/jp9057077 |
0.282 |
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| 2009 |
Saneyoshi H, Mazzini S, Aviñó A, Portella G, González C, Orozco M, Marquez VE, Eritja R. The use of conformationally rigid nucleoside probes to study the role of sugar pucker and nucleobase orientation in the thrombin binding aptamer. Nucleic Acids Symposium Series (2004). 109-10. PMID 19749284 DOI: 10.1093/nass/nrp055 |
0.339 |
|
| 2009 |
Faustino I, Aviño A, Marchán I, Luque FJ, Eritja R, Orozco M. Unique tautomeric and recognition properties of thioketothymines? Journal of the American Chemical Society. 131: 12845-53. PMID 19681616 DOI: 10.1021/ja904880y |
0.408 |
|
| 2009 |
Saneyoshi H, Mazzini S, Aviñó A, Portella G, González C, Orozco M, Marquez VE, Eritja R. Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer. Nucleic Acids Research. 37: 5589-601. PMID 19620215 DOI: 10.1093/nar/gkp598 |
0.371 |
|
| 2009 |
Talavera D, Orozco M, de la Cruz X. Alternative splicing of transcription factors' genes: beyond the increase of proteome diversity. Comparative and Functional Genomics. 905894. PMID 19609452 DOI: 10.1155/2009/905894 |
0.206 |
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| 2009 |
Soteras I, Forti F, Orozco M, Luque FJ. Performance of the IEF-MST solvation continuum model in a blind test prediction of hydration free energies. The Journal of Physical Chemistry. B. 113: 9330-4. PMID 19534454 DOI: 10.1021/jp903514u |
0.287 |
|
| 2009 |
Camps J, Carrillo O, Emperador A, Orellana L, Hospital A, Rueda M, Cicin-Sain D, D'Abramo M, Gelpí JL, Orozco M. FlexServ: an integrated tool for the analysis of protein flexibility. Bioinformatics (Oxford, England). 25: 1709-10. PMID 19429600 DOI: 10.1093/bioinformatics/btp304 |
0.745 |
|
| 2009 |
Klamt A, Mennucci B, Tomasi J, Barone V, Curutchet C, Orozco M, Luque FJ. On the performance of continuum solvation methods. A comment on "Universal approaches to solvation modeling". Accounts of Chemical Research. 42: 489-92; discussion 4. PMID 19222200 DOI: 10.1021/Ar800187P |
0.502 |
|
| 2009 |
Velázquez-Muriel JA, Rueda M, Cuesta I, Pascual-Montano A, Orozco M, Carazo JM. Comparison of molecular dynamics and superfamily spaces of protein domain deformation. Bmc Structural Biology. 9: 6. PMID 19220918 DOI: 10.1186/1472-6807-9-6 |
0.329 |
|
| 2009 |
Meyer T, de la Cruz X, Orozco M. An atomistic view to the gas phase proteome. Structure (London, England : 1993). 17: 88-95. PMID 19141285 DOI: 10.1016/j.str.2008.11.006 |
0.275 |
|
| 2009 |
Laughton CA, Orozco M, Vranken W. COCO: a simple tool to enrich the representation of conformational variability in NMR structures. Proteins. 75: 206-16. PMID 18831040 DOI: 10.1002/prot.22235 |
0.369 |
|
| 2009 |
Bidon-Chanal A, Huertas O, Orozco M, Luque FJ. Solvation enthalpies of neutral solutes in water and octanol Theoretical Chemistry Accounts. 123: 11-20. DOI: 10.1007/S00214-009-0534-Z |
0.222 |
|
| 2008 |
Cozzini P, Kellogg GE, Spyrakis F, Abraham DJ, Costantino G, Emerson A, Fanelli F, Gohlke H, Kuhn LA, Morris GM, Orozco M, Pertinhez TA, Rizzi M, Sotriffer CA. Target flexibility: an emerging consideration in drug discovery and design. Journal of Medicinal Chemistry. 51: 6237-55. PMID 18785728 DOI: 10.1021/Jm800562D |
0.243 |
|
| 2008 |
Soteras I, Lozano O, Escolano C, Orozco M, Amat M, Bosch J, Luque FJ. Structure-directed reversion in the pi-facial stereoselective alkylation of chiral bicyclic lactams. The Journal of Organic Chemistry. 73: 7756-63. PMID 18763825 DOI: 10.1021/jo801665k |
0.272 |
|
| 2008 |
Gros J, Aviñó A, Lopez de la Osa J, González C, Lacroix L, Pérez A, Orozco M, Eritja R, Mergny JL. 8-Amino guanine accelerates tetramolecular G-quadruplex formation. Chemical Communications (Cambridge, England). 2926-8. PMID 18566727 DOI: 10.1039/B801221K |
0.548 |
|
| 2008 |
Svozil D, Sponer JE, Marchan I, Pérez A, Cheatham TE, Forti F, Luque FJ, Orozco M, Sponer J. Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. The Journal of Physical Chemistry. B. 112: 8188-97. PMID 18558755 DOI: 10.1021/Jp801245H |
0.598 |
|
| 2008 |
Goñi JR, Fenollosa C, Pérez A, Torrents D, Orozco M. DNAlive: a tool for the physical analysis of DNA at the genomic scale. Bioinformatics (Oxford, England). 24: 1731-2. PMID 18544548 DOI: 10.1093/bioinformatics/btn259 |
0.593 |
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| 2008 |
Emperador A, Carrillo O, Rueda M, Orozco M. Exploring the suitability of coarse-grained techniques for the representation of protein dynamics. Biophysical Journal. 95: 2127-38. PMID 18487297 DOI: 10.1529/biophysj.107.119115 |
0.342 |
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| 2008 |
Soteras I, Orozco M, Luque FJ. Induction effects in metal cation-benzene complexes. Physical Chemistry Chemical Physics : Pccp. 10: 2616-24. PMID 18464976 DOI: 10.1039/b719461g |
0.303 |
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| 2008 |
Orozco M, Noy A, Pérez A. Recent advances in the study of nucleic acid flexibility by molecular dynamics. Current Opinion in Structural Biology. 18: 185-93. PMID 18304803 DOI: 10.1016/j.sbi.2008.01.005 |
0.58 |
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| 2008 |
Pérez A, Lankas F, Luque FJ, Orozco M. Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Research. 36: 2379-94. PMID 18299282 DOI: 10.1093/nar/gkn082 |
0.632 |
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| 2008 |
Noy A, Luque FJ, Orozco M. Theoretical analysis of antisense duplexes: determinants of the RNase H susceptibility. Journal of the American Chemical Society. 130: 3486-96. PMID 18298115 DOI: 10.1021/ja076734u |
0.329 |
|
| 2008 |
Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A, Wang D, Gibbons F, Gordon PM, Sensen CW, ... ... Orozco M, et al. Interoperability with Moby 1.0--it's better than sharing your toothbrush! Briefings in Bioinformatics. 9: 220-31. PMID 18238804 DOI: 10.1093/Bib/Bbn003 |
0.23 |
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| 2008 |
Vazquez-Mayagoita A, Huertas O, Fuentes-Cabrera M, Sumpter BG, Orozco M, Luque FJ. Ab initio study of naphtho-homologated DNA bases. The Journal of Physical Chemistry. B. 112: 2179-86. PMID 18225888 DOI: 10.1021/jp7095746 |
0.365 |
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| 2008 |
Aviñó A, Grimau MG, Alvira M, Eritja R, Gargallo R, Orozco M, González C. Triplex formation using oligonucleotide clamps carrying 8-aminopurines. Nucleosides, Nucleotides & Nucleic Acids. 26: 979-83. PMID 18058521 DOI: 10.1080/15257770701508398 |
0.344 |
|
| 2008 |
Carrillo O, Orozco M. GRID-MD-A tool for massive simulation of protein channels. Proteins. 70: 892-9. PMID 17803238 DOI: 10.1002/prot.21592 |
0.348 |
|
| 2008 |
Forti F, Barril X, Luque FJ, Orozco M. Extension of the MST continuum solvation model to the RM1 semiempirical Hamiltonian. Journal of Computational Chemistry. 29: 578-87. PMID 17705247 DOI: 10.1002/jcc.20814 |
0.289 |
|
| 2008 |
Muñoz-Muriedas J, Perspicace S, Bech N, Guccione S, Orozco M, Luque FJ. Hydrophobic molecular similarity from MST fractional contributions to the octanol/water partition coefficient. Journal of Computer-Aided Molecular Design. 19: 401-19. PMID 16231200 DOI: 10.1007/s10822-005-7928-3 |
0.331 |
|
| 2008 |
Cubero E, Luque FJ, Orozco M. Is polarization important in cation-pi interactions? Proceedings of the National Academy of Sciences of the United States of America. 95: 5976-80. PMID 9600902 DOI: 10.1073/PNAS.95.11.5976 |
0.283 |
|
| 2007 |
Goñi JR, Pérez A, Torrents D, Orozco M. Determining promoter location based on DNA structure first-principles calculations. Genome Biology. 8: R263. PMID 18072969 DOI: 10.1186/gb-2007-8-12-r263 |
0.608 |
|
| 2007 |
Pérez A, Luque FJ, Orozco M. Dynamics of B-DNA on the microsecond time scale. Journal of the American Chemical Society. 129: 14739-45. PMID 17985896 DOI: 10.1021/ja0753546 |
0.623 |
|
| 2007 |
Ortega JA, Blas JR, Orozco M, Grandas A, Pedroso E, Robles J. Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent. Organic Letters. 9: 4503-6. PMID 17915883 DOI: 10.1021/Ol701826X |
0.361 |
|
| 2007 |
Fort J, de la Ballina LR, Burghardt HE, Ferrer-Costa C, Turnay J, Ferrer-Orta C, Usón I, Zorzano A, Fernández-Recio J, Orozco M, Lizarbe MA, Fita I, Palacín M. The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane. The Journal of Biological Chemistry. 282: 31444-52. PMID 17724034 DOI: 10.1074/jbc.M704524200 |
0.589 |
|
| 2007 |
Talavera D, Hospital A, Orozco M, de la Cruz X. A procedure for identifying homologous alternative splicing events. Bmc Bioinformatics. 8: 260. PMID 17640387 DOI: 10.1186/1471-2105-8-260 |
0.268 |
|
| 2007 |
Rueda M, Chacón P, Orozco M. Thorough validation of protein normal mode analysis: a comparative study with essential dynamics. Structure (London, England : 1993). 15: 565-75. PMID 17502102 DOI: 10.1016/J.Str.2007.03.013 |
0.294 |
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| 2007 |
Noy A, Pérez A, Laughton CA, Orozco M. Theoretical study of large conformational transitions in DNA: the B<-->A conformational change in water and ethanol/water. Nucleic Acids Research. 35: 3330-8. PMID 17459891 DOI: 10.1093/nar/gkl1135 |
0.596 |
|
| 2007 |
Pérez A, Marchán I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M. Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophysical Journal. 92: 3817-29. PMID 17351000 DOI: 10.1529/Biophysj.106.097782 |
0.587 |
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| 2007 |
Talavera D, Vogel C, Orozco M, Teichmann SA, de la Cruz X. The (in)dependence of alternative splicing and gene duplication. Plos Computational Biology. 3: e33. PMID 17335345 DOI: 10.1371/Journal.Pcbi.0030033 |
0.284 |
|
| 2007 |
Soliva R, Gelpí JL, Almansa C, Virgili M, Orozco M. Dissection of the recognition properties of p38 MAP kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor family. Journal of Medicinal Chemistry. 50: 283-93. PMID 17228870 DOI: 10.1021/JM061073H |
0.269 |
|
| 2007 |
Rueda M, Ferrer-Costa C, Meyer T, Pérez A, Camps J, Hospital A, Gelpí JL, Orozco M. A consensus view of protein dynamics. Proceedings of the National Academy of Sciences of the United States of America. 104: 796-801. PMID 17215349 DOI: 10.1073/pnas.0605534104 |
0.607 |
|
| 2007 |
Blas JR, López-Bes JM, Márquez M, Sessler JL, Luque FJ, Orozco M. Exploring the dynamics of calix[4]pyrrole: effect of solvent and fluorine substitution. Chemistry (Weinheim An Der Bergstrasse, Germany). 13: 1108-16. PMID 17086569 DOI: 10.1002/Chem.200600757 |
0.334 |
|
| 2007 |
Muñoz-Muriedas J, Barril X, López JM, Orozco M, Luque FJ. A hydrophobic similarity analysis of solvation effects on nucleic acid bases. Journal of Molecular Modeling. 13: 357-65. PMID 17024407 DOI: 10.1007/s00894-006-0150-y |
0.676 |
|
| 2007 |
Curutchet C, Bidon-Chanal A, Soteras I, Orozco M, Luque FJ. MST continuum study of the hydration free energies of monovalent ionic species. The Journal of Physical Chemistry. B. 109: 3565-74. PMID 16851394 DOI: 10.1021/JP047197S |
0.274 |
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| 2007 |
Soteras I, Lozano O, Gómez-Esqué A, Escolano C, Orozco M, Amat M, Bosch J, Luque FJ. On the origin of the stereoselectivity in the alkylation of oxazolopiperidone enolates. Journal of the American Chemical Society. 128: 6581-8. PMID 16704257 DOI: 10.1021/JA055393M |
0.272 |
|
| 2007 |
Huertas O, Blas JR, Soteras I, Orozco M, Luque FJ. Benzoderivatives of nucleic acid bases as modified DNA building blocks. The Journal of Physical Chemistry. A. 110: 510-8. PMID 16405323 DOI: 10.1021/JP052126U |
0.359 |
|
| 2006 |
Meyer T, Ferrer-Costa C, Pérez A, Rueda M, Bidon-Chanal A, Luque FJ, Laughton CA, Orozco M. Essential Dynamics: A Tool for Efficient Trajectory Compression and Management. Journal of Chemical Theory and Computation. 2: 251-8. PMID 26626512 DOI: 10.1021/ct050285b |
0.587 |
|
| 2006 |
Huertas O, Poater J, Fuentes-Cabrera M, Orozco M, Solà M, Luque FJ. Local aromaticity in natural nucleobases and their size-expanded benzo-fused derivatives. The Journal of Physical Chemistry. A. 110: 12249-58. PMID 17078622 DOI: 10.1021/Jp063790T |
0.315 |
|
| 2006 |
Ferrer-Costa C, Orozco M, de la Cruz X. Characterization of compensated mutations in terms of structural and physico-chemical properties. Journal of Molecular Biology. 365: 249-56. PMID 17059831 DOI: 10.1016/J.JMB.2006.09.053 |
0.252 |
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| 2006 |
Talavera D, Morreale A, Meyer T, Hospital A, Ferrer-Costa C, Gelpi JL, de la Cruz X, Soliva R, Luque FJ, Orozco M. A fast method for the determination of fractional contributions to solvation in proteins. Protein Science : a Publication of the Protein Society. 15: 2525-33. PMID 17001031 DOI: 10.1110/Ps.062406706 |
0.354 |
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| 2006 |
Curutchet C, Orozco M, Luque FJ, Mennucci B, Tomasi J. Dispersion and repulsion contributions to the solvation free energy: comparison of quantum mechanical and classical approaches in the polarizable continuum model. Journal of Computational Chemistry. 27: 1769-80. PMID 16917857 DOI: 10.1002/Jcc.20480 |
0.517 |
|
| 2006 |
Bidon-Chanal A, Martí MA, Crespo A, Milani M, Orozco M, Bolognesi M, Luque FJ, Estrin DA. Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N Proteins: Structure, Function and Genetics. 64: 457-464. PMID 16688782 DOI: 10.1002/Prot.21004 |
0.299 |
|
| 2006 |
Goñi JR, Vaquerizas JM, Dopazo J, Orozco M. Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions. Bmc Genomics. 7: 63. PMID 16566817 DOI: 10.1186/1471-2164-7-63 |
0.273 |
|
| 2006 |
Rueda M, Luque FJ, Orozco M. G-quadruplexes can maintain their structure in the gas phase. Journal of the American Chemical Society. 128: 3608-19. PMID 16536534 DOI: 10.1021/JA055936S |
0.36 |
|
| 2006 |
Sponer J, Jurecka P, Marchan I, Luque FJ, Orozco M, Hobza P. Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps. Chemistry (Weinheim An Der Bergstrasse, Germany). 12: 2854-65. PMID 16425171 DOI: 10.1002/Chem.200501239 |
0.35 |
|
| 2006 |
Noy A, Meyer T, Rueda M, Ferrer C, Valencia A, Pérez A, de la Cruz X, López-Bes JM, Pouplana R, Fernandez-Recio J, Luque FJ, Orozco M. Data mining of molecular dynamics trajectories of nucleic acids. Journal of Biomolecular Structure & Dynamics. 23: 447-56. PMID 16363879 DOI: 10.1080/07391102.2006.10507070 |
0.602 |
|
| 2006 |
López de la Osa J, González C, Gargallo R, Rueda M, Cubero E, Orozco M, Aviñó A, Eritja R. Destabilization of quadruplex DNA by 8-aminoguanine. Chembiochem : a European Journal of Chemical Biology. 7: 46-8. PMID 16292787 DOI: 10.1002/cbic.200500281 |
0.3 |
|
| 2006 |
Ferrer-Costa C, Orozco M, de la Cruz X. Use of bioinformatics tools for the annotation of disease-associated mutations in animal models. Proteins. 61: 878-87. PMID 16208716 DOI: 10.1002/prot.20664 |
0.246 |
|
| 2006 |
Pérez A, Sponer J, Jurecka P, Hobza P, Luque FJ, Orozco M. Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study. Chemistry (Weinheim An Der Bergstrasse, Germany). 11: 5062-6. PMID 15977281 DOI: 10.1002/Chem.200500255 |
0.591 |
|
| 2006 |
Muñoz-Muriedas J, Lopez JM, Orozco M, Luque FJ. Molecular modelling approaches to the design of acetylcholinesterase inhibitors: new challenges for the treatment of Alzheimer's disease. Current Pharmaceutical Design. 10: 3131-40. PMID 15544503 DOI: 10.2174/1381612043383386 |
0.276 |
|
| 2006 |
Ferrer-Costa C, Orozco M, de la Cruz X. Sequence-based prediction of pathological mutations. Proteins. 57: 811-9. PMID 15390262 DOI: 10.1002/prot.20252 |
0.293 |
|
| 2006 |
Fuentes-Cabrera M, Lipkowski P, Huertas O, Sumpter BG, Orozco M, Luque FJ, Wells JC, Leszczynski J. Aromaticity-induced changes in electronic properties of size-expanded DNA bases: Case of xC International Journal of Quantum Chemistry. 106: 2339-2346. DOI: 10.1002/Qua.20966 |
0.316 |
|
| 2005 |
Pérez A, Blas JR, Rueda M, López-Bes JM, de la Cruz X, Orozco M. Exploring the Essential Dynamics of B-DNA. Journal of Chemical Theory and Computation. 1: 790-800. PMID 26641895 DOI: 10.1021/ct050051s |
0.623 |
|
| 2005 |
Cubero E, Luque FJ, Orozco M. Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA. Biophysical Journal. 90: 1000-8. PMID 16287814 DOI: 10.1529/BIOPHYSJ.105.059535 |
0.426 |
|
| 2005 |
Muñoz-Ruiz P, Rubio L, García-Palomero E, Dorronsoro I, del Monte-Millán M, Valenzuela R, Usán P, de Austria C, Bartolini M, Andrisano V, Bidon-Chanal A, Orozco M, Luque FJ, Medina M, Martínez A. Design, synthesis, and biological evaluation of dual binding site acetylcholinesterase inhibitors: new disease-modifying agents for Alzheimer's disease. Journal of Medicinal Chemistry. 48: 7223-33. PMID 16279781 DOI: 10.1021/Jm0503289 |
0.221 |
|
| 2005 |
Alonso D, Dorronsoro I, Rubio L, Muñoz P, García-Palomero E, Monte MD, Bidon-Chanal A, Orozco M, Luque FJ, Castro A, Medina M, Martínez A. Donepezil–tacrine hybrid related derivatives as new dual binding site inhibitors of AChE Bioorganic & Medicinal Chemistry. 13: 6588-6597. PMID 16230018 DOI: 10.1016/J.Bmc.2005.09.029 |
0.249 |
|
| 2005 |
Rueda M, Luque FJ, Orozco M. Nature of minor-groove binders-DNA complexes in the gas phase. Journal of the American Chemical Society. 127: 11690-8. PMID 16104746 DOI: 10.1021/JA0422110 |
0.381 |
|
| 2005 |
Conde L, Vaquerizas JM, Ferrer-Costa C, de la Cruz X, Orozco M, Dopazo J. PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. Nucleic Acids Research. 33: W501-5. PMID 15980522 DOI: 10.1093/Nar/Gki476 |
0.246 |
|
| 2005 |
Ferrer-Costa C, Gelpí JL, Zamakola L, Parraga I, de la Cruz X, Orozco M. PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinformatics (Oxford, England). 21: 3176-8. PMID 15879453 DOI: 10.1093/bioinformatics/bti486 |
0.277 |
|
| 2005 |
Noy A, Pérez A, Márquez M, Luque FJ, Orozco M. Structure, recognition properties, and flexibility of the DNA.RNA hybrid. Journal of the American Chemical Society. 127: 4910-20. PMID 15796556 DOI: 10.1021/ja043293v |
0.6 |
|
| 2005 |
Crespo A, Martí MA, Kalko SG, Morreale A, Orozco M, Gelpi JL, Luque FJ, Estrin DA. Theoretical study of the truncated hemoglobin HbN: exploring the molecular basis of the NO detoxification mechanism. Journal of the American Chemical Society. 127: 4433-44. PMID 15783226 DOI: 10.1021/Ja0450004 |
0.322 |
|
| 2005 |
Morreale A, de la Cruz X, Meyer T, Gelpí JL, Luque FJ, Orozco M. Partition of protein solvation into group contributions from molecular dynamics simulations. Proteins. 58: 101-9. PMID 15517587 DOI: 10.1002/prot.20292 |
0.394 |
|
| 2005 |
Stollar EJ, Gelpí JL, Velankar S, Golovin A, Orozco M, Luisi BF. Unconventional interactions between water and heterocyclic nitrogens in protein structures. Proteins. 57: 1-8. PMID 15326588 DOI: 10.1002/prot.20216 |
0.296 |
|
| 2005 |
Soteras I, Curutchet C, Bidon-Chanal A, Orozco M, Luque FJ. Extension of the MST model to the IEF formalism: HF and B3LYP parametrizations Journal of Molecular Structure: Theochem. 727: 29-40. DOI: 10.1016/J.THEOCHEM.2005.02.029 |
0.228 |
|
| 2004 |
Pérez A, Noy A, Lankas F, Luque FJ, Orozco M. The relative flexibility of B-DNA and A-RNA duplexes: database analysis. Nucleic Acids Research. 32: 6144-51. PMID 15562006 DOI: 10.1093/nar/gkh954 |
0.597 |
|
| 2004 |
Spacková N, Cubero E, Sponer J, Orozco M. Theoretical study of the guanine --> 6-thioguanine substitution in duplexes, triplexes, and tetraplexes. Journal of the American Chemical Society. 126: 14642-50. PMID 15521784 DOI: 10.1021/JA0468628 |
0.324 |
|
| 2004 |
Noy A, Pérez A, Lankas F, Javier Luque F, Orozco M. Relative flexibility of DNA and RNA: a molecular dynamics study. Journal of Molecular Biology. 343: 627-38. PMID 15465050 DOI: 10.1016/j.jmb.2004.07.048 |
0.621 |
|
| 2004 |
Morreale A, de la Cruz X, Meyer T, Gelpí JL, Luque FJ, Orozco M. Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories? Proteins. 57: 458-67. PMID 15382247 DOI: 10.1002/prot.20169 |
0.359 |
|
| 2004 |
Marti L, Abella A, De La Cruz X, García-Vicente S, Unzeta M, Carpéné C, Palacín M, Testar X, Orozco M, Zorzano A. Exploring the binding mode of semicarbazide-sensitive amine oxidase/VAP-1: identification of novel substrates with insulin-like activity. Journal of Medicinal Chemistry. 47: 4865-74. PMID 15369390 DOI: 10.1021/JM0499211 |
0.234 |
|
| 2004 |
Rueda M, Cubero E, Laughton CA, Orozco M. Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations? Biophysical Journal. 87: 800-11. PMID 15298889 DOI: 10.1529/biophysj.104.040451 |
0.379 |
|
| 2004 |
Marco JL, de los RÃos C, GarcÃa AG, Villarroya M, Carreiras MC, Martins C, Eleutério A, Morreale A, Orozco M, Luque FJ. Synthesis, biological evaluation and molecular modelling of diversely functionalized heterocyclic derivatives as inhibitors of acetylcholinesterase/butyrylcholinesterase and modulators of Ca2+ channels and nicotinic receptors. Bioorganic & Medicinal Chemistry. 12: 2199-218. PMID 15080920 DOI: 10.1016/j.bmc.2004.02.017 |
0.237 |
|
| 2004 |
Gómez-Pinto I, Cubero E, Kalko SG, Monaco V, van der Marel G, van Boom JH, Orozco M, González C. Effect of bulky lesions on DNA: solution structure of a DNA duplex containing a cholesterol adduct. The Journal of Biological Chemistry. 279: 24552-60. PMID 15047709 DOI: 10.1074/jbc.M311751200 |
0.406 |
|
| 2004 |
Goñi JR, de la Cruz X, Orozco M. Triplex-forming oligonucleotide target sequences in the human genome. Nucleic Acids Research. 32: 354-60. PMID 14726484 DOI: 10.1093/NAR/GKH188 |
0.251 |
|
| 2004 |
Estévez R, Pusch M, Ferrer-Costa C, Orozco M, Jentsch TJ. Functional and structural conservation of CBS domains from CLC chloride channels. The Journal of Physiology. 557: 363-78. PMID 14724190 DOI: 10.1113/Jphysiol.2003.058453 |
0.23 |
|
| 2004 |
Blas JR, Luque FJ, Orozco M. Unique tautomeric properties of isoguanine. Journal of the American Chemical Society. 126: 154-64. PMID 14709079 DOI: 10.1021/JA036806R |
0.306 |
|
| 2004 |
Aviñó A, Cubero E, González C, Eritja R, Orozco M. Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives. Journal of the American Chemical Society. 125: 16127-38. PMID 14678005 DOI: 10.1021/JA035039T |
0.396 |
|
| 2004 |
Valenzuela A, Talavera D, Orozco M, de la Cruz X. Alternative splicing mechanisms for the modulation of protein function: conservation between human and other species. Journal of Molecular Biology. 335: 495-502. PMID 14672658 DOI: 10.1016/J.Jmb.2003.10.061 |
0.243 |
|
| 2004 |
Cubero E, Abrescia NG, Subirana JA, Luque FJ, Orozco M. Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex. Journal of the American Chemical Society. 125: 14603-12. PMID 14624611 DOI: 10.1021/JA035918F |
0.411 |
|
| 2004 |
Curutchet C, Bofill JM, Hernández B, Orozco M, Luque FJ. Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations. Journal of Computational Chemistry. 24: 1263-75. PMID 12820134 DOI: 10.1002/Jcc.10260 |
0.306 |
|
| 2004 |
Soteras I, Morreale A, López JM, Orozco M, Luque FJ. Group contributions to the solvation free energy from MST continuum calculations Brazilian Journal of Physics. 34: 48-57. DOI: 10.1590/S0103-97332004000100008 |
0.243 |
|
| 2004 |
Curutchet C, Bidon-Chanal A, Orozco M, Luque F. MST study of group contributions for alkane derivatives: effect of the charge normalization Chemical Physics Letters. 384: 299-305. DOI: 10.1016/J.CPLETT.2003.12.041 |
0.22 |
|
| 2004 |
Orozco M, Perez A, Noy A, Luque FJ. Theoretical Methods for the Simulation of Nucleic Acids Cheminform. 35. DOI: 10.1002/CHIN.200405276 |
0.288 |
|
| 2004 |
Avino A, Frieden M, Morales JC, de la Torre BG, Gueimil-Garcia R, Orozco M, Gonzalez C, Eritja R. Properties of Triple Helices Formed by Oligonucleotides Containing 8-Aminopurines Cheminform. 35. DOI: 10.1002/CHIN.200402222 |
0.278 |
|
| 2003 |
Orozco M, Pérez A, Noy A, Luque FJ. Theoretical methods for the simulation of nucleic acids. Chemical Society Reviews. 32: 350-64. PMID 14671790 DOI: 10.1039/b207226m |
0.607 |
|
| 2003 |
Aviñó A, Frieden M, Morales JC, de la Torre BG, Güimil-García R, Orozco M, González C, Eritja R. Properties of triple helices formed by oligonucleotides containing 8-aminopurines. Nucleosides, Nucleotides & Nucleic Acids. 22: 645-8. PMID 14565244 DOI: 10.1081/NCN-120021971 |
0.297 |
|
| 2003 |
Morreale A, Gelpí JL, Luque FJ, Orozco M. Continuum and discrete calculation of fractional contributions to solvation free energy. Journal of Computational Chemistry. 24: 1610-23. PMID 12926005 DOI: 10.1002/jcc.10323 |
0.35 |
|
| 2003 |
Rueda M, Kalko SG, Luque FJ, Orozco M. The structure and dynamics of DNA in the gas phase. Journal of the American Chemical Society. 125: 8007-14. PMID 12823023 DOI: 10.1021/JA0300564 |
0.397 |
|
| 2003 |
Fradera X, Márquez M, Smith BD, Orozco M, Luque FJ. Molecular dynamics study of 2rotaxanes: influence of solvation and cation on co-conformation. The Journal of Organic Chemistry. 68: 4663-73. PMID 12790569 DOI: 10.1021/Jo034457D |
0.379 |
|
| 2003 |
Escaja N, Gelpí JL, Orozco M, Rico M, Pedroso E, González C. Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad. Journal of the American Chemical Society. 125: 5654-62. PMID 12733903 DOI: 10.1021/Ja0344157 |
0.369 |
|
| 2003 |
Soliva R, Almansa C, Kalko SG, Luque FJ, Orozco M. Theoretical studies on the inhibition mechanism of cyclooxygenase-2. Is there a unique recognition site? Journal of Medicinal Chemistry. 46: 1372-82. PMID 12672237 DOI: 10.1021/JM0209376 |
0.29 |
|
| 2003 |
Salichs A, López M, Segarra V, Orozco M, Luque FJ. Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study. Journal of Computer-Aided Molecular Design. 16: 569-83. PMID 12602951 DOI: 10.1023/A:1021975932288 |
0.265 |
|
| 2003 |
Curutchet C, Cramer CJ, Truhlar DG, Ruiz-López MF, Rinaldi D, Orozco M, Luque FJ. Electrostatic component of solvation: comparison of SCRF continuum models. Journal of Computational Chemistry. 24: 284-97. PMID 12548720 DOI: 10.1002/Jcc.10143 |
0.308 |
|
| 2003 |
Curutchet C, Salichs A, Barril X, Orozco M, Javier Luque F. Transferability of fragmental contributions to the octanol/water partition coefficient: an NDDO-based MST study. Journal of Computational Chemistry. 24: 32-45. PMID 12483673 DOI: 10.1002/jcc.10155 |
0.297 |
|
| 2003 |
Ribas J, Cubero E, Luque FJ, Orozco M. Theoretical study of alkyl-pi and aryl-pi interactions. Reconciling theory and experiment. The Journal of Organic Chemistry. 67: 7057-65. PMID 12354000 DOI: 10.1021/JO0201225 |
0.287 |
|
| 2003 |
Luque FJ, Curutchet C, Muñoz-Muriedas J, Bidon-Chanal A, Soteras I, Morreale A, Gelpí JL, Orozco M. Continuum solvation models: Dissecting the free energy of solvation Physical Chemistry Chemical Physics. 5: 3827-3836. DOI: 10.1039/b306954k |
0.31 |
|
| 2003 |
Cubero E, Luque FJ, Orozco M, Gao J. Perturbation Approach to Combined QM/MM Simulation of Solute−Solvent Interactions in Solution The Journal of Physical Chemistry B. 107: 1664-1671. DOI: 10.1021/Jp026874K |
0.355 |
|
| 2003 |
Fradera X, De Rosa M, Orozco M, Luque FJ. Tautomeric conjugate acids of 2-aminopyrroles: effect of substituents, solvation and cosolute Theoretical Chemistry Accounts. 111: 223-230. DOI: 10.1007/S00214-003-0508-5 |
0.236 |
|
| 2003 |
Fradera X, Marquez M, Smith BD, Orozco M, Luque FJ. Molecular Dynamics Study of [2]Rotaxanes: Influence of Solvation and Cation on Co-conformation. Cheminform. 34. DOI: 10.1002/CHIN.200338047 |
0.367 |
|
| 2002 |
Blas JR, Márquez M, Sessler JL, Luque FJ, Orozco M. Theoretical study of anion binding to calix[4]pyrrole: the effects of solvent, fluorine substitution, cosolute, and water traces. Journal of the American Chemical Society. 124: 12796-805. PMID 12392426 DOI: 10.1021/Ja020318M |
0.321 |
|
| 2002 |
Barril X, Orozco M, Luque FJ. Towards improved acetylcholinesterase inhibitors: a structural and computational approach. Mini Reviews in Medicinal Chemistry. 1: 255-66. PMID 12369972 DOI: 10.2174/1389557013406828 |
0.276 |
|
| 2002 |
Barril X, Kalko SG, Orozco M, Luque FJ. Rational design of reversible acetylcholinesterase inhibitors. Mini Reviews in Medicinal Chemistry. 2: 27-36. PMID 12369955 DOI: 10.2174/1389557023406494 |
0.266 |
|
| 2002 |
Fradera X, De La Cruz X, Silva CH, Gelpí JL, Luque FJ, Orozco M. Ligand-induced changes in the binding sites of proteins. Bioinformatics (Oxford, England). 18: 939-48. PMID 12117791 DOI: 10.1093/BIOINFORMATICS/18.7.939 |
0.3 |
|
| 2002 |
Aviñó A, Frieden M, Morales JC, García de la Torre B, Güimil García R, Azorín F, Gelpí JL, Orozco M, González C, Eritja R. Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines. Nucleic Acids Research. 30: 2609-19. PMID 12060677 DOI: 10.1093/NAR/GKF374 |
0.298 |
|
| 2002 |
Muñoz J, Barril X, Hernández B, Orozco M, Luque FJ. Hydrophobic similarity between molecules: a MST-based hydrophobic similarity index. Journal of Computational Chemistry. 23: 554-63. PMID 11948582 DOI: 10.1002/jcc.10055 |
0.338 |
|
| 2002 |
Cubero E, Aviñó A, de la Torre BG, Frieden M, Eritja R, Luque FJ, González C, Orozco M. Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives. Journal of the American Chemical Society. 124: 3133-42. PMID 11902902 DOI: 10.1021/JA011928+ |
0.409 |
|
| 2002 |
Rueda M, Luque FJ, Orozco M. A theoretical investigation on the effect of remote amino groups in hydrogen bonding of nucleic acids. Biopolymers. 61: 52-60. PMID 11891628 DOI: 10.1002/1097-0282(2001)61:1<52::AID-BIP10046>3.0.CO;2-2 |
0.277 |
|
| 2002 |
Dvir H, Wong DM, Harel M, Barril X, Orozco M, Luque FJ, Muñoz-Torrero D, Camps P, Rosenberry TL, Silman I, Sussman JL. 3D structure of Torpedo californica acetylcholinesterase complexed with huprine X at 2.1 A resolution: kinetic and molecular dynamic correlates. Biochemistry. 41: 2970-81. PMID 11863435 DOI: 10.1021/Bi011652I |
0.29 |
|
| 2002 |
Ferrer-Costa C, Orozco M, de la Cruz X. Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties. Journal of Molecular Biology. 315: 771-86. PMID 11812146 DOI: 10.1006/JMBI.2001.5255 |
0.312 |
|
| 2002 |
Gelpí JL, Kalko SG, Barril X, Cirera J, de La Cruz X, Luque FJ, Orozco M. Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins. Proteins. 45: 428-37. PMID 11746690 DOI: 10.1002/prot.1159 |
0.378 |
|
| 2002 |
Camps P, Gómez E, Muñoz-Torrero D, Badia A, Vivas NM, Barril X, Orozco M, Luque FJ. Synthesis, in vitro pharmacology, and molecular modeling of syn-huprines as acetylcholinesterase inhibitors. Journal of Medicinal Chemistry. 44: 4733-6. PMID 11741490 DOI: 10.1021/JM010949B |
0.298 |
|
| 2002 |
Cubero E, Luque FJ, Orozco M. Theoretical studies of d(A:T)-based parallel-stranded DNA duplexes. Journal of the American Chemical Society. 123: 12018-25. PMID 11724610 DOI: 10.1021/JA011200T |
0.399 |
|
| 2002 |
Kalko SG, Gelpí JL, Fita I, Orozco M. Theoretical study of the mechanisms of substrate recognition by catalase. Journal of the American Chemical Society. 123: 9665-72. PMID 11572688 DOI: 10.1021/JA010512T |
0.292 |
|
| 2002 |
Robles J, Grandas A, Pedroso E, Luque F, Eritja R, Orozco M. Nucleic Acid Triple Helices: Stability Effects of Nucleobase Modifications Current Organic Chemistry. 6: 1333-1368. DOI: 10.2174/1385272023373482 |
0.262 |
|
| 2002 |
Hernández B, Curutchet C, Colominas C, Orozco M, Luque FJ. Prediction of Conformational Free Energy Differences of Solutes in Solution∶ An MC-MST Study Molecular Simulation. 28: 153-171. DOI: 10.1080/08927020211979 |
0.269 |
|
| 2002 |
Trygubenko SA, Bogdan TV, Rueda M, Orozco M, Luque FJ, Poner J, Ek PS, Hobza P. Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solutionDedicated to the memory of our friend and distinguished scientist Professor Peter Kollman. Physical Chemistry Chemical Physics. 4: 4192-4203. DOI: 10.1039/B202156K |
0.237 |
|
| 2002 |
Muñoz J, Gelpí JL, Soler-López M, Subirana JA, Orozco M, Luque FJ. Can Divalent Metal Cations Stabilize the Triplex Motif? Theoretical Study of the Interaction of the Hydrated Mg2+ Cation with the G−G·C Triplet The Journal of Physical Chemistry B. 106: 8849-8857. DOI: 10.1021/JP026096W |
0.244 |
|
| 2001 |
Harris SA, Gavathiotis E, Searle MS, Orozco M, Laughton CA. Cooperativity in drug-DNA recognition: a molecular dynamics study. Journal of the American Chemical Society. 123: 12658-63. PMID 11741431 DOI: 10.1021/Ja016233N |
0.417 |
|
| 2001 |
Soliva R, Monaco V, Gómez-Pinto I, Meeuwenoord NJ, Van Der Marel GA, Van Boom JH, González C, Orozco M. Solution structure of a DNA duplex with a chiral alkyl phosphonate moiety Nucleic Acids Research. 29: 2973-2985. PMID 11452022 DOI: 10.1093/Nar/29.14.2973 |
0.405 |
|
| 2001 |
Aviñó A, Morales JC, Frieden M, de la Torre BG, García RG, Cubero E, Luque FJ, Orozco M, Azorín F, Eritja R. Parallel-stranded hairpins containing 8-aminopurines. Novel efficient probes for triple-helix formation. Bioorganic & Medicinal Chemistry Letters. 11: 1761-3. PMID 11425555 DOI: 10.1016/S0960-894X(01)00295-5 |
0.311 |
|
| 2001 |
Cubero E, Güimil-García R, Luque FJ, Eritja R, Orozco M. The effect of amino groups on the stability of DNA duplexes and triplexes based on purines derived from inosine. Nucleic Acids Research. 29: 2522-34. PMID 11410660 DOI: 10.1093/NAR/29.12.2522 |
0.352 |
|
| 2001 |
Hernández B, Soliva R, Luque FJ, Orozco M. Misincorporation of 2'-deoxyoxanosine into DNA: a molecular basis for NO-induced mutagenesis derived from theoretical calculations. Nucleic Acids Research. 28: 4873-83. PMID 11121478 DOI: 10.1093/NAR/28.24.4873 |
0.358 |
|
| 2001 |
Camps P, Morral J, Muñoz-Torrero D, Badia A, Baños JE, Vivas NM, Barril X, Orozco M, Luque FJ. New tacrine-huperzine A hybrids (huprines): highly potent tight-binding acetylcholinesterase inhibitors of interest for the treatment of Alzheimer's disease. Journal of Medicinal Chemistry. 43: 4657-66. PMID 11101357 DOI: 10.1021/JM000980Y |
0.256 |
|
| 2001 |
Busquets C, Merinero B, Christensen E, Gelpí JL, Campistol J, Pineda M, Fernández-Alvarez E, Prats JM, Sans A, Arteaga R, Martí M, Campos J, Martínez-Pardo M, Martínez-Bermejo A, Ruiz-Falcó ML, ... ... Orozco M, et al. Glutaryl-CoA dehydrogenase deficiency in Spain: evidence of two groups of patients, genetically, and biochemically distinct. Pediatric Research. 48: 315-22. PMID 10960496 DOI: 10.1203/00006450-200009000-00009 |
0.246 |
|
| 2001 |
Guàrdia E, Pinzón R, Casulleras J, Orozco M, Luque FJ. Comparison of Different Three-site Interaction Potentials for Liquid Acetonitrile Molecular Simulation. 26: 287-306. DOI: 10.1080/08927020108024509 |
0.231 |
|
| 2001 |
Rueda M, Luque FJ, López JM, Orozco M. Amino−Imino Tautomerism in Derivatives of Cytosine: Effect on Hydrogen-Bonding and Stacking Properties The Journal of Physical Chemistry A. 105: 6575-6580. DOI: 10.1021/JP010838O |
0.239 |
|
| 2001 |
Barril X, Gelpí JL, López JM, Orozco M, Luque FJ. How accurate can molecular dynamics/linear response and Poisson-Boltzmann/solvent accessible surface calculations be for predicting relative binding affinities? Acetylcholinesterase huprine inhibitors as a test case Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 106: 2-9. DOI: 10.1007/S002140000216 |
0.298 |
|
| 2001 |
Curutchet C, Orozco M, Luque FJ. Solvation in octanol: parametrization of the continuum MST model Journal of Computational Chemistry. 22: 1180-1193. DOI: 10.1002/jcc.1076 |
0.228 |
|
| 2001 |
Lavilla R, Coll O, Bosch J, Orozco M, Luque F. General Access to Tacamine and Vinca-Eburna Alkaloids through Tandem Non-Biomimetic Oxidation of Dihydropyridines/Zn-Mediated Radical Addition Processes − Unexpected Facial Selectivity of Flattened Cyclohexyl-Type Radicals European Journal of Organic Chemistry. 2001: 3719. DOI: 10.1002/1099-0690(200110)2001:19<3719::AID-EJOC3719>3.0.CO;2-W |
0.206 |
|
| 2000 |
Soliva R, Güimil García R, Blas JR, Eritja R, Asensio JL, González C, Luque FJ, Orozco M. DNA-triplex stabilizing properties of 8-aminoguanine. Nucleic Acids Research. 28: 4531-9. PMID 11071942 DOI: 10.1093/NAR/28.22.4531 |
0.374 |
|
| 2000 |
Hernández B, Luque FJ, Orozco M. Mixed QM/MM molecular electrostatic potentials. Journal of Computer-Aided Molecular Design. 14: 329-39. PMID 10815770 DOI: 10.1023/A:1008111820916 |
0.325 |
|
| 2000 |
Amat M, Bosch J, Hidalgo J, Cantó M, Pérez M, Llor N, Molins E, Miravitlles C, Orozco M, Luque J. Synthesis of enantiopure trans-3,4-disubstituted piperidines. An enantiodivergent synthesis of (+)- and (-)-paroxetine. The Journal of Organic Chemistry. 65: 3074-84. PMID 10814199 DOI: 10.1021/JO991816P |
0.218 |
|
| 2000 |
Barril X, Orozco M, Luque FJ. Predicting relative binding free energies of tacrine-huperzine A hybrids as inhibitors of acetylcholinesterase. Journal of Medicinal Chemistry. 42: 5110-9. PMID 10602696 DOI: 10.1021/JM990371U |
0.302 |
|
| 2000 |
Barril X, Muñoz J, Javier Luque F, Orozco M. Simplified descriptions of the topological distribution of hydrophilic/hydrophobic characteristics of molecules Physical Chemistry Chemical Physics. 2: 4897-4905. DOI: 10.1039/B000020P |
0.254 |
|
| 2000 |
Soliva R, Sherer E, Luque FJ, Laughton CA, Orozco M. Molecular dynamics simulations of PNA·DNA and PNA·RNA duplexes in aqueous solution Journal of the American Chemical Society. 122: 5997-6008. DOI: 10.1021/Ja000259H |
0.385 |
|
| 2000 |
Cubero E, Laughton CA, Luque FJ, Orozco M. Molecular Dynamics Study of Oligonucleotides Containing Difluorotoluene Journal of the American Chemical Society. 122: 6891-6899. DOI: 10.1021/JA000117N |
0.343 |
|
| 2000 |
Luque FJ, López JM, Orozco M. Perspective on "Electrostatic interactions of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects" Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 103: 343-345. DOI: 10.1007/s002149900013 |
0.309 |
|
| 1999 |
Colominas C, Luque FJ, Orozco M. Monte Carlo-MST: New strategy for representation of solvent configurational space in solution. Journal of Computational Chemistry. 20: 665-678. PMID 34376037 DOI: 10.1002/(SICI)1096-987X(199905)20:7<665::AID-JCC2>3.0.CO;2-W |
0.295 |
|
| 1999 |
Soliva R, Luque FJ, Alhambra C, Orozco M. Role of sugar re-puckering in the transition of A and B forms of DNA in solution. A molecular dynamics study. Journal of Biomolecular Structure & Dynamics. 17: 89-99. PMID 10496424 DOI: 10.1080/07391102.1999.10508343 |
0.39 |
|
| 1999 |
Camps P, El Achab R, Görbig DM, Morral J, Muñoz-Torrero D, Badia A, Eladi Baños J, Vivas NM, Barril X, Orozco M, Luque FJ. Synthesis, in vitro pharmacology, and molecular modeling of very potent tacrine-huperzine A hybrids as acetylcholinesterase inhibitors of potential interest for the treatment of Alzheimer's disease. Journal of Medicinal Chemistry. 42: 3227-42. PMID 10464010 DOI: 10.1021/JM980620Z |
0.249 |
|
| 1999 |
Soliva R, Luque FJ, Orozco M. Can G-C Hoogsteen-wobble pairs contribute to the stability of d(G. C-C) triplexes? Nucleic Acids Research. 27: 2248-55. PMID 10325411 DOI: 10.1093/NAR/27.11.2248 |
0.278 |
|
| 1999 |
García RG, Ferrer E, Macías MJ, Eritja R, Orozco M. Theoretical calculations, synthesis and base pairing properties of oligonucleotides containing 8-amino-2'-deoxyadenosine. Nucleic Acids Research. 27: 1991-8. PMID 10198432 DOI: 10.1093/NAR/27.9.1991 |
0.355 |
|
| 1999 |
Luque FJ, Barril X, Orozco M. Fractional description of free energies of solvation. Journal of Computer-Aided Molecular Design. 13: 139-52. PMID 10091120 DOI: 10.1023/A:1008036526741 |
0.294 |
|
| 1999 |
Güimil García R, Bachi A, Eritja R, Luque FJ, Orozco M. Triple helix stabilization properties of oligonucleotides containing 8-amino-2'-deoxyguanosine. Bioorganic & Medicinal Chemistry Letters. 8: 3011-6. PMID 9873666 DOI: 10.1016/S0960-894X(98)00537-X |
0.295 |
|
| 1999 |
Eritja R, Ferrer E, García RG, Orozco M. Modified Oligonucleotides with Triple-Helix Stabilization Properties Nucleosides and Nucleotides. 18: 1619-1621. DOI: 10.1080/07328319908044801 |
0.26 |
|
| 1999 |
De Rosa M, Issac RP, Marquez M, Orozco M, Luque FJ, Timken MD. 2-Aminopyrrole and simple 1-substituted 2-aminopyrroles: Preparation and ab initio study on the effect of solvent on the amino-imino tautomeric equilibrium Journal of the Chemical Society. Perkin Transactions 2. 1433-1437. DOI: 10.1039/A900762H |
0.715 |
|
| 1999 |
Cubero E, Orozco M, Luque FJ. A Topological Analysis of Electron Density in Cation−π Complexes The Journal of Physical Chemistry A. 103: 6054-6054. DOI: 10.1021/JP991792Q |
0.208 |
|
| 1999 |
Colominas C, Luque FJ, Orozco M. Dimerization of Formamide in Gas Phase and Solution. An Ab Initio MC−MST Study The Journal of Physical Chemistry A. 103: 6200-6208. DOI: 10.1021/JP9908092 |
0.229 |
|
| 1999 |
Cubero E, Orozco M, Hobza P, Luque FJ. Hydrogen Bond versus Anti-Hydrogen Bond: A Comparative Analysis Based on the Electron Density Topology The Journal of Physical Chemistry A. 103: 6394-6401. DOI: 10.1021/JP990258F |
0.229 |
|
| 1999 |
Forés M, Duran aM, Solà M, Orozco M, Luque FJ. Theoretical Evaluation of Solvent Effects on the Conformational and Tautomeric Equilibria of 2-(2'-Hydroxyphenyl)benzimidazole and on Its Absorption and Fluorescence Spectra Journal of Physical Chemistry A. 103: 4525-4532. DOI: 10.1021/Jp984773+ |
0.313 |
|
| 1999 |
Cubero E, Sherer EC, Luque FJ, Orozco M, Laughton CA. Observation of spontaneous base pair breathing events in the molecular dynamics simulation of a difluorotoluene-containing DNA oligonucleotide [5] Journal of the American Chemical Society. 121: 8653-8654. DOI: 10.1021/Ja991067T |
0.361 |
|
| 1999 |
Shields GC, Laughton CA, Orozco M. Molecular Dynamics Simulation of a PNA·DNA·PNA Triple Helix in Aqueous SolutionJ. Am. Chem. Soc.1998,120, 5895−5904 Journal of the American Chemical Society. 121: 1625-1625. DOI: 10.1021/JA985540Z |
0.342 |
|
| 1999 |
Sherer EC, Harris SA, Soliva R, Orozco M, Laughton CA. Molecular dynamics studies of DNA A-tract structure and flexibility Journal of the American Chemical Society. 121: 5981-5991. DOI: 10.1021/Ja983715Z |
0.42 |
|
| 1999 |
Colominas C, Luque F, Teixidó J, Orozco M. Cavitation contribution to the free energy of solvation. Chemical Physics. 240: 253-264. DOI: 10.1016/S0301-0104(98)00333-4 |
0.231 |
|
| 1999 |
Cubero E, Orozco M, Luque F. Electron density topological analysis of the C–H⋯O anti-hydrogen bond in the fluoroform–oxirane complex Chemical Physics Letters. 310: 445-450. DOI: 10.1016/S0009-2614(99)00831-3 |
0.229 |
|
| 1999 |
Hern�ndez B, Luque FJ, Orozco M. Parametrization of the GMIPp for the study of stacking interactions Journal of Computational Chemistry. 20: 937-946. DOI: 10.1002/(SICI)1096-987X(19990715)20:9<937::AID-JCC5>3.0.CO;2-W |
0.231 |
|
| 1998 |
Jiménez-García E, Vaquero A, Espinás ML, Soliva R, Orozco M, Bernués J, Azorín F. The GAGA factor of Drosophila binds triple-stranded DNA. The Journal of Biological Chemistry. 273: 24640-8. PMID 9733760 DOI: 10.1074/jbc.273.38.24640 |
0.338 |
|
| 1998 |
Barril X, Alemán C, Orozco M, Luque FJ. Salt bridge interactions: stability of the ionic and neutral complexes in the gas phase, in solution, and in proteins. Proteins. 32: 67-79. PMID 9672043 DOI: 10.1002/(SICI)1097-0134(19980701)32:1<67::AID-PROT8>3.0.CO;2-B |
0.316 |
|
| 1998 |
Luisi B, Orozco M, Sponer J, Luque FJ, Shakked Z. On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules. Journal of Molecular Biology. 279: 1123-1136. PMID 9642089 DOI: 10.1006/Jmbi.1998.1833 |
0.305 |
|
| 1998 |
Luque FJ, López JM, López de la Paz M, Vicent C, Orozco M. Role of Intramolecular Hydrogen Bonds in the Intermolecular Hydrogen Bonding of Carbohydrates The Journal of Physical Chemistry A. 102: 6690-6696. DOI: 10.1021/JP981690K |
0.219 |
|
| 1998 |
Orozco M, Hernández B, Luque FJ. Tautomerism of 1-Methyl Derivatives of Uracil, Thymine, and 5-Bromouracil. Is Tautomerism the Basis for the Mutagenicity of 5-Bromouridine? The Journal of Physical Chemistry B. 102: 5228-5233. DOI: 10.1021/JP981005+ |
0.228 |
|
| 1998 |
Colominas C, Teixidó J, Cemelí J, Luque FJ, Orozco M. Dimerization of Carboxylic Acids: Reliability of Theoretical Calculations and the Effect of Solvent The Journal of Physical Chemistry B. 102: 2269-2276. DOI: 10.1021/JP973414W |
0.265 |
|
| 1998 |
Colominas C, Orozco M, Luque FJ, Borrell JI, Teixidó J. A Priori Prediction of Substituent and Solvent Effects in the Basicity of Nitriles The Journal of Organic Chemistry. 63: 4947-4953. DOI: 10.1021/JO972354N |
0.237 |
|
| 1998 |
Cubero E, Orozco M, Luque FJ. Azidoazomethine−Tetrazole Isomerism in Solution: A Thermochemical Study The Journal of Organic Chemistry. 63: 2354-2356. DOI: 10.1021/JO971576I |
0.211 |
|
| 1998 |
Soliva R, Laughton CA, Luque FJ, Orozco M. Molecular Dynamics Simulations in Aqueous Solution of Triple Helices Containing d(G·C·C) Trios Journal of the American Chemical Society. 120: 11226-11233. DOI: 10.1021/JA981121Q |
0.335 |
|
| 1998 |
Cubero E, Orozco M, Luque FJ. Theoretical Study of Azido−Tetrazole Isomerism: Effect of Solvent and Substituents and Mechanism of Isomerization Journal of the American Chemical Society. 120: 4723-4731. DOI: 10.1021/JA9726724 |
0.273 |
|
| 1998 |
Shields GC, Laughton CA, Orozco M. Molecular Dynamics Simulation of a PNA·DNA·PNA Triple Helix in Aqueous Solution Journal of the American Chemical Society. 120: 5895-5904. DOI: 10.1021/JA9723444 |
0.342 |
|
| 1998 |
Luque FJ, Orozco M. Polarization effects in generalized molecular interaction potential: New Hamiltonian for reactivity studies and mixed QM/MM calculations Journal of Computational Chemistry. 19: 866-881. DOI: 10.1002/(SICI)1096-987X(199806)19:8<866::AID-JCC6>3.0.CO;2-N |
0.289 |
|
| 1997 |
Orozco M, Vega C, Parraga A, García-Sáez I, Coll M, Walsh S, Mantle TJ, Javier Luque F. On the reaction mechanism of class Pi glutathione S-transferase. Proteins. 28: 530-42. PMID 9261869 DOI: 10.1002/(SICI)1097-0134(199708)28:4<530::AID-PROT7>3.0.CO;2-D |
0.321 |
|
| 1997 |
Tirado-Rives J, Orozco M, Jorgensen WL. Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea. Biochemistry. 36: 7313-29. PMID 9200680 DOI: 10.1021/Bi970096I |
0.399 |
|
| 1997 |
Alemán C, Roca R, Luque FJ, Orozco M. Helical preferences of alanine, glycine, and aminoisobutyric homopeptides. Proteins. 28: 83-93. PMID 9144793 DOI: 10.1002/(SICI)1097-0134(199705)28:1<83::AID-PROT8>3.0.CO;2-K |
0.28 |
|
| 1997 |
Hernández B, Orozco M, Luque FJ. Role of tautomerism of 2-azaadenine and 2-azahypoxanthine in substrate recognition by xanthine oxidase. Journal of Computer-Aided Molecular Design. 11: 153-62. PMID 9089433 DOI: 10.1023/A:1008082425628 |
0.288 |
|
| 1997 |
Hernández B, Orozco M, Luque FJ. Tautomerism of xanthine and alloxanthine: a model for substrate recognition by xanthine oxidase. Journal of Computer-Aided Molecular Design. 10: 535-44. PMID 9007687 DOI: 10.1007/BF00134177 |
0.308 |
|
| 1997 |
Luque FJ, Bofill JM, Orozco M. Response to “Comment on ‘New strategies to incorporate the solvent polarization in self-consistent reaction field and free-energy perturbation simulations’ ” [J. Chem. Phys. 107, 1291 (1997)] The Journal of Chemical Physics. 107: 1293-1294. DOI: 10.1063/1.474478 |
0.267 |
|
| 1997 |
Alhambra C, Luque FJ, Gago F, Orozco M. Ab InitioStudy of Stacking Interactions in A- and B-DNA The Journal of Physical Chemistry B. 101: 3846-3853. DOI: 10.1021/JP962626A |
0.298 |
|
| 1997 |
Luque FJ, Orozco M. Semiclassical-Continuum Approach to the Electrostatic Free Energy of Solvation The Journal of Physical Chemistry B. 101: 5573-5582. DOI: 10.1021/JP9617229 |
0.249 |
|
| 1997 |
Shields GC, Laughton CA, Orozco M. Molecular Dynamics Simulations of the d(T·A·T) Triple Helix Journal of the American Chemical Society. 119: 7463-7469. DOI: 10.1021/JA970601Z |
0.336 |
|
| 1997 |
Orozco M, Luque F. Generalized linear response approximation in discrete methods Chemical Physics Letters. 265: 473-480. DOI: 10.1016/S0009-2614(96)01429-7 |
0.211 |
|
| 1997 |
Soliva R, Luque FJ, Orozco M. Reliability of MEP and MEP-derived properties computed from DFT methods for molecules containing P, S and CL Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 98: 42-49. DOI: 10.1007/S002140050276 |
0.252 |
|
| 1997 |
Luque FJ, López-Bes JM, Cemeli J, Aroztegui M, Orozco M. Solvent effects on tautomerism equilibria in heterocycles Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 96: 105-113. DOI: 10.1007/S002140050210 |
0.242 |
|
| 1997 |
Soliva R, Orozco M, Luque FJ. Suitability of density functional methods for calculation of electrostatic properties Journal of Computational Chemistry. 18: 980-991. DOI: 10.1002/(SICI)1096-987X(199706)18:8<980::AID-JCC2>3.0.CO;2-M |
0.247 |
|
| 1996 |
Luque FJ, Zhang Y, Alemán C, Bachs M, Gao J, Orozco M. Solvent Effects in Chloroform Solution: Parametrization of the MST/SCRF Continuum Model The Journal of Physical Chemistry. 100: 4269-4276. DOI: 10.1021/JP9529331 |
0.238 |
|
| 1996 |
Mestres J, Solà M, Carbó R, Luque FJ, Orozco M. Effect of Solvation on the Charge Distribution of a Series of Anionic, Neutral, and Cationic Species. A Quantum Molecular Similarity Study The Journal of Physical Chemistry. 100: 606-610. DOI: 10.1021/Jp9519169 |
0.262 |
|
| 1996 |
Hernández B, Luque FJ, Orozco M. Tautomerism of Xanthine Oxidase Substrates Hypoxanthine and Allopurinol The Journal of Organic Chemistry. 61: 5964-5971. DOI: 10.1021/JO960133W |
0.181 |
|
| 1996 |
Colominas C, Luque FJ, Orozco M. Tautomerism and Protonation of Guanine and Cytosine. Implications in the Formation of Hydrogen-Bonded Complexes Journal of the American Chemical Society. 118: 6811-6821. DOI: 10.1021/JA954293L |
0.239 |
|
| 1996 |
Orozco M, Roca R, Alemán C, Busquets M, López J, Luque F. Theoretical representation of solvent effects in the study of biochemical systems Journal of Molecular Structure: Theochem. 371: 269-278. DOI: 10.1016/S0166-1280(96)04529-0 |
0.237 |
|
| 1996 |
Orozco M, Colominas C, Luque FJ. Theoretical determination of the solvation free energy in water and chloroform of the nucleic acid bases Chemical Physics. 209: 19-29. DOI: 10.1016/0301-0104(96)00112-7 |
0.263 |
|
| 1996 |
Camps P, Luque FJ, Orozco M, Pérez F, Vázquez S. Synthesis, chemical trapping and dimerization of tricyclo[3.3.0.03,7]oct-1(5)-ene, the consummate member of a series of pyramidalized alkenes Tetrahedron Letters. 37: 8605-8608. DOI: 10.1016/0040-4039(96)01967-3 |
0.228 |
|
| 1996 |
Orozco M, Alhambra C, Barril X, L�pez J, Busquets M, Luque F. Theoretical Methods for the Representation of Solvent Journal of Molecular Modeling. 2: 1-15. DOI: 10.1007/S0089460020001 |
0.251 |
|
| 1996 |
Orozco M, L�pez JM, Colomines C, Alhambra C, Busquets MA, Luque FJ. Theoretical representation of solvation in biochemical systems: From discrete solute-solvent interactions to bulk solvation International Journal of Quantum Chemistry. 60: 1179-1187. DOI: 10.1002/(SICI)1097-461X(1996)60:6<1179::AID-QUA6>3.0.CO;2-X |
0.262 |
|
| 1996 |
Luque FJ, Bachs M, Alem�n C, Orozco M. Extension of MST/SCRF method to organic solvents:Ab initio and semiempirical parametrization for neutral solutes in CCl4 Journal of Computational Chemistry. 17: 806-820. DOI: 10.1002/(SICI)1096-987X(199605)17:7<806::AID-JCC5>3.0.CO;2-W |
0.251 |
|
| 1995 |
Gallego J, Luque FJ, Orozco M, Gago F. Binding of echinomycin to d(GCGC)2 and d(CCGG)2: distinct stacking interactions dictate the sequence-dependent formation of Hoogsteen base pairs. Journal of Biomolecular Structure & Dynamics. 12: 111-29. PMID 7848562 DOI: 10.1080/07391102.1994.10508091 |
0.363 |
|
| 1995 |
Alhambra C, Luque FJ, Portugal J, Orozco M. Molecular dynamics study of the binding of elsamicin A to DNA. European Journal of Biochemistry. 230: 555-66. PMID 7607229 DOI: 10.1111/J.1432-1033.1995.0555H.X |
0.384 |
|
| 1995 |
Orozco M, Luque FJ, Habibollahzadeh D, Gao J. Erratum: The polarization contribution to the free energy of hydration [J. Chem. Phys. 102, 6145 (1995)] The Journal of Chemical Physics. 103: 9112-9113. DOI: 10.1063/1.470732 |
0.239 |
|
| 1995 |
Luque FJ, Bofill JM, Orozco M. New strategies to incorporate the solvent polarization in self‐consistent reaction field and free‐energy perturbation simulations The Journal of Chemical Physics. 103: 10183-10191. DOI: 10.1063/1.469921 |
0.299 |
|
| 1995 |
Orozco M, Luque FJ, Habibollahzadeh D, Gao J. The polarization contribution to the free energy of hydration The Journal of Chemical Physics. 102: 6145-6152. DOI: 10.1063/1.469348 |
0.278 |
|
| 1995 |
Alhambra C, Luque FJ, Estelrich J, Orozco M. Tautomerism of Neutral and Protonated 6-Thioguanine in the Gas Phase and in Aqueous Solution. An ab Initio Study The Journal of Organic Chemistry. 60: 969-976. DOI: 10.1021/JO00109A031 |
0.233 |
|
| 1995 |
Orozco M, Luque FJ. Theoretical Study of the Tautomerism and Protonation of 7-Aminopyrazolopyrimidine in the Gas Phase and in Aqueous Solution Journal of the American Chemical Society. 117: 1378-1386. DOI: 10.1021/JA00109A023 |
0.225 |
|
| 1995 |
Laughton CA, Luque FJ, Orozco M. Counterion Distribution around DNA Studied by Molecular Dynamics and Quantum Mechanical Simulations The Journal of Physical Chemistry. 99: 11591-11599. DOI: 10.1021/J100029A042 |
0.355 |
|
| 1995 |
Luque FJ, Alhambra C, Orozco M. Effect of Solvent Polarization on Bimolecular Interactions The Journal of Physical Chemistry. 99: 11344-11349. DOI: 10.1021/J100029A008 |
0.238 |
|
| 1995 |
Alhambra C, Luque FJ, Orozco M. Molecular Solvation Potential. A New Tool for the Quantum Mechanical Description of Hydration in Organic and Bioorganic Molecules The Journal of Physical Chemistry. 99: 3084-3092. DOI: 10.1021/J100010A018 |
0.287 |
|
| 1995 |
Miguel D, Diez A, Blache Y, Luque J, Orozco M, Remuson R, Gelas-Mialhe Y, Rubiralta M. Synthetic studies on indole alkaloids VIII. 1 Synthesis and reactivity of asymmetric 2-indolyi-4-methylenepiperidines Tetrahedron. 51: 7527-7546. DOI: 10.1016/0040-4020(95)00376-J |
0.21 |
|
| 1995 |
Bastida J, Codina C, Peeters P, Rubiralta M, Orozco M, Luque F, Chhabra S. Alkaloids from Crinum kirkii Phytochemistry. 40: 1291-1293. DOI: 10.1016/0031-9422(95)00391-J |
0.183 |
|
| 1995 |
Luque F, Gadre S, Bhadane P, Orozco M. The effect of hydration on the molecular charge distribution of cations. An ab initio SCRF study Chemical Physics Letters. 232: 509-517. DOI: 10.1016/0009-2614(94)01403-I |
0.521 |
|
| 1995 |
Orozco M, Bachs M, Luque FJ. Development of optimized MST/SCRF methods for semiempirical calculations: The MNDO and PM3 Hamiltonians Journal of Computational Chemistry. 16: 563-575. DOI: 10.1002/jcc.540160505 |
0.222 |
|
| 1994 |
Gallego J, Luque FJ, Orozco M, Burgos C, Alvarez-Builla J, Rodrigo MM, Gago F. DNA sequence-specific reading by echinomycin: role of hydrogen bonding and stacking interactions. Journal of Medicinal Chemistry. 37: 1602-9. PMID 8201593 DOI: 10.1021/JM00037A010 |
0.365 |
|
| 1994 |
Luque FJ, Orozco M, Bhadane PK, Gadre SR. Effect of solvation on the shapes, sizes, and anisotropies of polyatomic anions via molecular electrostatic potential topography: Anab initioself‐consistent reaction field approach The Journal of Chemical Physics. 100: 6718-6726. DOI: 10.1063/1.467032 |
0.544 |
|
| 1994 |
Alemán C, Orozco M, Luque F. Multicentric charges for the accurate representation of electrostatic interactions in force-field calculations for small molecules Chemical Physics. 189: 573-584. DOI: 10.1016/0301-0104(94)00310-6 |
0.274 |
|
| 1994 |
Orozco M, Luque F. Optimization of the cavity size for ab initio MST-SCRF calculations of monovalent ions Chemical Physics. 182: 237-248. DOI: 10.1016/0301-0104(94)00029-8 |
0.214 |
|
| 1994 |
Luque FJ, Bachs M, Orozco M. An optimized AM1/MST method for the MST-SCRF representation of solvated systems Journal of Computational Chemistry. 15: 847-857. DOI: 10.1002/jcc.540150806 |
0.21 |
|
| 1994 |
Bachs M, Luque FJ, Orozco M. Optimization of solute cavities and van der Waals parameters inab initio MST-SCRF calculations of neutral molecules Journal of Computational Chemistry. 15: 446-454. DOI: 10.1002/jcc.540150408 |
0.247 |
|
| 1994 |
Alhambra C, Luque FJ, Orozco M. Comparison of NDDO and quasi-ab initio approaches to compute semiempirical molecular electrostatic potentials Journal of Computational Chemistry. 15: 12-22. DOI: 10.1002/jcc.540150103 |
0.305 |
|
| 1994 |
Alemán C, Orozco M. PAPQMD/AM1 Parametrization of the bonded term of aromatic biomolecules Biopolymers. 34: 941-955. DOI: 10.1002/BIP.360340712 |
0.222 |
|
| 1993 |
Orozco M, Tirado-Rives J, Jorgensen WL. Mechanism for the rotamase activity of FK506 binding protein from molecular dynamics simulations. Biochemistry. 32: 12864-74. PMID 8251509 DOI: 10.1021/Bi00210A040 |
0.349 |
|
| 1993 |
Gao J, Luque FJ, Orozco M. Induced dipole moment and atomic charges based on average electrostatic potentials in aqueous solution The Journal of Chemical Physics. 98: 2975-2982. DOI: 10.1063/1.464126 |
0.35 |
|
| 1993 |
Luque FJ, Orozco M. Theoretical study of N-methylacetamide in vacuum and aqueous solution: implications for the peptide bond isomerization The Journal of Organic Chemistry. 58: 6397-6405. DOI: 10.1021/JO00075A039 |
0.229 |
|
| 1993 |
Luque FJ, Orozco M, Bhadane PK, Gadre SR. SCRF calculation of the effect of water on the topology of the molecular electrostatic potential The Journal of Physical Chemistry. 97: 9380-9384. DOI: 10.1021/J100139A021 |
0.503 |
|
| 1993 |
Luque FJ, Negre MJ, Orozco M. An AM1-SCRF approach to the study of changes in molecular properties induced by solvent The Journal of Physical Chemistry. 97: 4386-4391. DOI: 10.1021/J100119A022 |
0.294 |
|
| 1993 |
Alem�n C, Luque FJ, Orozco M. A new scaling procedure to correct semiempirical MEP and MEP-derived properties Journal of Computer-Aided Molecular Design. 7: 721-742. DOI: 10.1007/BF00125328 |
0.218 |
|
| 1993 |
Orozco M, Jorgensen WL, Luque F. Comparison of 6-31G*-based MST/SCRF and FEP evaluations of the free energies of hydration for small neutral molecules Journal of Computational Chemistry. 14: 1498-1503. DOI: 10.1002/Jcc.540141212 |
0.29 |
|
| 1993 |
Carlson HA, Nguyen TB, Orozco M, Jorgensen WL. Accuracy of free energies of hydration for organic molecules from 6-31g*-derived partial charges Journal of Computational Chemistry. 14: 1240-1249. DOI: 10.1002/Jcc.540141013 |
0.289 |
|
| 1993 |
Orozco M, Luque F. Ab initio study of bond stretching: Implications in force-field parametrization for molecular mechanics and dynamics Journal of Computational Chemistry. 14: 881-894. DOI: 10.1002/jcc.540140802 |
0.323 |
|
| 1993 |
Alemán C, Luque F, Orozco M. Suitability of the PM3-derived molecular electrostatic potentials Journal of Computational Chemistry. 14: 799-808. DOI: 10.1002/JCC.540140706 |
0.283 |
|
| 1993 |
Orozco M, Luque F. Molecular interaction potential: A new tool for the theoretical study of molecular reactivity Journal of Computational Chemistry. 14: 587-602. DOI: 10.1002/jcc.540140512 |
0.31 |
|
| 1993 |
Orozco M, Luque FJ. Self-consistent reaction field computation of the reactive characteristics of DNA bases in water Biopolymers. 33: 1851-1869. DOI: 10.1002/BIP.360331211 |
0.278 |
|
| 1992 |
Alemán C, Orozco M. On the suitability of semiempirical calculations as sources of force field parameters. Journal of Computer-Aided Molecular Design. 6: 331-48. PMID 1403027 DOI: 10.1007/BF00125943 |
0.241 |
|
| 1992 |
Rubiralta M, Luque J, Orozco M, Diez A, L用ez I. Conformational Analysis of 2-Aryl-4-piperidones. Effect of the Indole Protective Phenylsulfonyl Group Heterocycles. 34: 449. DOI: 10.3987/COM-91-5955 |
0.254 |
|
| 1992 |
Orozco M, Luque F. A practical approach to the computation of the electrostatic energy in large molecules Journal of Molecular Structure: Theochem. 254: 31-42. DOI: 10.1016/0166-1280(92)80049-R |
0.261 |
|
| 1992 |
Negre M, Orozco M, Luque F. A new strategy for the representation of environment effects in semi-empirical calculations based on Dewar's Hamiltonians Chemical Physics Letters. 196: 27-36. DOI: 10.1016/0009-2614(92)85924-Y |
0.244 |
|
| 1991 |
Orozco M, Luque FJ. A practical procedure for the determination of electrostatic charges of large molecules. Journal of Computer-Aided Molecular Design. 4: 411-26. PMID 2092084 DOI: 10.1007/BF00117406 |
0.279 |
|
| 1991 |
Luque FJ, Orozco M, Illas F, Rubio J. Effect of electron correlation on the electrostatic potential distribution of molecules Journal of the American Chemical Society. 113: 5203-5211. DOI: 10.1021/JA00014A010 |
0.232 |
|
| 1991 |
Alemán C, Canela EI, Franco R, Orozco M. A new strategy for the evaluation of force parameters from quantum mechanical computations Journal of Computational Chemistry. 12: 664-674. DOI: 10.1002/JCC.540120603 |
0.229 |
|
| 1990 |
Orozco M, Lluis C, Mallol J, Canela EI, Franco R. Quantum chemical study of the electronic and conformational characteristics of adenosine and 8-substituted derivatives: functional implications in the mechanism of reaction of adenosine deaminase. Journal of Pharmaceutical Sciences. 79: 133-7. PMID 2324961 DOI: 10.1002/JPS.2600790212 |
0.317 |
|
| 1990 |
Orozco M, Canela EI, Franco R. A quantum chemical study of the enzymatic deamination of benzoadenine derivatives. A theoretical model of the interactions occurring between nucleosides and the active site of adenosine deaminase. European Journal of Biochemistry. 188: 155-63. PMID 2156693 DOI: 10.1111/J.1432-1033.1990.TB15383.X |
0.287 |
|
| 1990 |
Orozco M, Canela EI, Franco R. Theoretical study of the hydroxyl nucleophilic attack on the 6-aminopyrimidine molecule: functional implications in the reaction mechanism of nucleoside deaminative enzymes The Journal of Organic Chemistry. 55: 2630-2637. DOI: 10.1021/JO00296A018 |
0.246 |
|
| 1990 |
Orozco M, Canela EI, Mallol J, Lluis C, Franco R. Ab initio study of the protonation and the tautomerism of the 7-aminopyrazolopyrimidine molecule The Journal of Organic Chemistry. 55: 753-756. DOI: 10.1021/JO00289A061 |
0.272 |
|
| 1990 |
Orozco M, Velasco D, Canela EI, Franco R. Determination of the conformational preferences of adenosine at the active site of adenosine deaminase Journal of the American Chemical Society. 112: 8221-8229. DOI: 10.1021/JA00179A001 |
0.239 |
|
| 1990 |
Orozco M, Franco R. Computer simulated process of "lead optimization": A student-interactive program Journal of Chemical Education. 67: 232. DOI: 10.1021/ed067p232 |
0.227 |
|
| 1990 |
Orozco M, Franco R, Mallol J, Canela E. Theoretical study of the acidic strength of amino acid side chains Bioorganic Chemistry. 18: 361-372. DOI: 10.1016/0045-2068(90)90020-6 |
0.223 |
|
| 1990 |
Luque F, Orozco M. Reliability of the AM1 wavefunction to compute molecular electrostatic potentials Chemical Physics Letters. 168: 269-275. DOI: 10.1016/0009-2614(90)85609-G |
0.28 |
|
| 1990 |
Orozco M, Luque FJ. On the use of AM1 and MNDO wave functions to compute accurate electrostatic charges Journal of Computational Chemistry. 11: 909-923. DOI: 10.1002/JCC.540110803 |
0.219 |
|
| 1990 |
Luque FJ, Illas F, Orozco M. Comparative study of the molecular electrostatic potential obtained from different wavefunctions. Reliability of the semiempirical MNDO wavefunction Journal of Computational Chemistry. 11: 416-430. DOI: 10.1002/JCC.540110403 |
0.297 |
|
| 1989 |
Orozco M, Luque FJ. POEAMS: program for outliers elimination in 'anomalous' multidimensional space. Computer Applications in the Biosciences : Cabios. 5: 241-2. PMID 2766013 DOI: 10.1093/bioinformatics/5.3.241 |
0.183 |
|
| 1989 |
Orozco M, Franco R. TEFOOL/2: a program for theoretical drug design on microcomputers. Computer Applications in the Biosciences : Cabios. 5: 219-26. PMID 2766007 DOI: 10.1093/bioinformatics/5.3.219 |
0.218 |
|
| 1989 |
Orozco M, Luque F. On the use of mixed basis sets to compute accurate molecular electrostatic potentials Chemical Physics Letters. 160: 305-310. DOI: 10.1016/0009-2614(89)87601-8 |
0.282 |
|
| 1989 |
Orozco M, Lluis C, Mallol J, Canela EI, Franco R. Theoretical Approximation to the Reaction Mechanism of Adenosine Deaminase Quantitative Structure-Activity Relationships. 8: 109-114. DOI: 10.1002/QSAR.19890080206 |
0.213 |
|
| 1988 |
Orozco M, Luque FJ. POEMS: program for outliers elimination in multidimensional space. Computer Applications in the Biosciences : Cabios. 4: 381-5. PMID 3416200 DOI: 10.1093/BIOINFORMATICS/4.3.381 |
0.225 |
|
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