| Year |
Citation |
Score |
| 2023 |
Schimunek J, Seidl P, Elez K, Hempel T, Le T, Noé F, Olsson S, Raich L, Winter R, Gokcan H, Gusev F, Gutkin EM, Isayev O, Kurnikova MG, Narangoda CH, ... ... Wade R, et al. A community effort in SARS-CoV-2 drug discovery. Molecular Informatics. PMID 37833243 DOI: 10.1002/minf.202300262 |
0.774 |
|
| 2023 |
Mukesh S, Mukherjee G, Singh R, Steenbuck N, Demidova C, Joshi P, Sangamwar AT, Wade RC. Comparative analysis of drug-salt-polymer interactions by experiment and molecular simulation improves biopharmaceutical performance. Communications Chemistry. 6: 201. PMID 37749228 DOI: 10.1038/s42004-023-01006-0 |
0.65 |
|
| 2023 |
Viviani LG, Kokh DB, Wade RC, T-do Amaral A. Molecular Dynamics Simulations of the Human Ecto-5'-Nucleotidase (h-ecto-5'-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics. Journal of Chemical Information and Modeling. 63: 4691-4707. PMID 37532679 DOI: 10.1021/acs.jcim.3c01068 |
0.702 |
|
| 2023 |
Claveras Cabezudo A, Athanasiou C, Tsengenes A, Wade RC. Scaling Protein-Water Interactions in the Martini 3 Coarse-Grained Force Field to Simulate Transmembrane Helix Dimers in Different Lipid Environments. Journal of Chemical Theory and Computation. PMID 36821400 DOI: 10.1021/acs.jctc.2c00950 |
0.796 |
|
| 2023 |
Tanvir Rahman M, Kristian Koski M, Panecka-Hofman J, Schmitz W, Kastaniotis AJ, Wade RC, Wierenga RK, Kalervo Hiltunen J, Autio KJ. An engineered variant of MECR reductase reveals indispensability of long-chain acyl-ACPs for mitochondrial respiration. Nature Communications. 14: 619. PMID 36739436 DOI: 10.1038/s41467-023-36358-7 |
0.77 |
|
| 2022 |
Panecka-Hofman J, Poehner I, Wade R. Anti-trypanosomatid structure-based drug design - lessons learned from targeting the folate pathway. Expert Opinion On Drug Discovery. PMID 36073204 DOI: 10.1080/17460441.2022.2113776 |
0.776 |
|
| 2022 |
Pöhner I, Quotadamo A, Panecka-Hofman J, Luciani R, Santucci M, Linciano P, Landi G, Di Pisa F, Dello Iacono L, Pozzi C, Mangani S, Gul S, Witt G, Ellinger B, Kuzikov M, ... ... Wade RC, et al. Multitarget, Selective Compound Design Yields Potent Inhibitors of a Kinetoplastid Pteridine Reductase 1. Journal of Medicinal Chemistry. PMID 35675511 DOI: 10.1021/acs.jmedchem.2c00232 |
0.778 |
|
| 2022 |
Rogdakis T, Charou D, Latorrata A, Papadimitriou E, Tsengenes A, Athanasiou C, Papadopoulou M, Chalikiopoulou C, Katsila T, Ramos I, Prousis KC, Wade RC, Sidiropoulou K, Calogeropoulou T, Gravanis A, et al. Development and Biological Characterization of a Novel Selective TrkA Agonist with Neuroprotective Properties against Amyloid Toxicity. Biomedicines. 10. PMID 35327415 DOI: 10.3390/biomedicines10030614 |
0.751 |
|
| 2021 |
Sadiq SK, Muñiz Chicharro A, Friedrich P, Wade RC. Multiscale Approach for Computing Gated Ligand Binding from Molecular Dynamics and Brownian Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 34739248 DOI: 10.1021/acs.jctc.1c00673 |
0.301 |
|
| 2021 |
Kokh DB, Wade RC. G Protein-Coupled Receptor-Ligand Dissociation Rates and Mechanisms from τRAMD Simulations. Journal of Chemical Theory and Computation. PMID 34495672 DOI: 10.1021/acs.jctc.1c00641 |
0.712 |
|
| 2021 |
Bianciotto M, Gkeka P, Kokh DB, Wade RC, Minoux H. Contact Map Fingerprints of Protein-Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics. Journal of Chemical Theory and Computation. PMID 34494849 DOI: 10.1021/acs.jctc.1c00453 |
0.702 |
|
| 2021 |
De M, Öztürk MA, Isbaner S, Tóth K, Wade RC. DNA sequence-dependent positioning of the linker histone in a nucleosome: a single-pair FRET study. Biophysical Journal. PMID 34293303 DOI: 10.1016/j.bpj.2021.07.012 |
0.383 |
|
| 2021 |
Nunes-Alves A, Kokh DB, Wade RC. Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations. Current Research in Structural Biology. 3: 106-111. PMID 34235490 DOI: 10.1016/j.crstbi.2021.04.001 |
0.709 |
|
| 2021 |
Nunes-Alves A, Ormersbach F, Wade RC. Prediction of the Drug-Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis. Journal of Chemical Information and Modeling. PMID 34197096 DOI: 10.1021/acs.jcim.1c00639 |
0.33 |
|
| 2021 |
Gossen J, Albani S, Hanke A, Joseph BP, Bergh C, Kuzikov M, Costanzi E, Manelfi C, Storici P, Gribbon P, Beccari AR, Talarico C, Spyrakis F, Lindahl E, Zaliani A, ... ... Wade RC, et al. A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics. Acs Pharmacology & Translational Science. 4: 1079-1095. PMID 34136757 DOI: 10.1021/acsptsci.0c00215 |
0.717 |
|
| 2021 |
Glaser M, Bruce NJ, Han SB, Wade RC. Simulation of the Positive Inotropic Peptide S100A1ct in Aqueous Environment by Gaussian Accelerated Molecular Dynamics. The Journal of Physical Chemistry. B. PMID 33944558 DOI: 10.1021/acs.jpcb.1c00902 |
0.549 |
|
| 2021 |
Reinhardt M, Bruce NJ, Kokh DB, Wade RC. Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics. Journal of Chemical Theory and Computation. PMID 33784462 DOI: 10.1021/acs.jctc.0c01312 |
0.772 |
|
| 2021 |
Ganotra GK, Nunes-Alves A, Wade RC. A Protocol to Use Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time. Methods in Molecular Biology (Clifton, N.J.). 2266: 171-186. PMID 33759127 DOI: 10.1007/978-1-0716-1209-5_10 |
0.806 |
|
| 2021 |
Berger BT, Amaral M, Kokh DB, Nunes-Alves A, Musil D, Heinrich T, Schröder M, Neil R, Wang J, Navratilova I, Bomke J, Elkins JM, Müller S, Frech M, Wade RC, et al. Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2. Cell Chemical Biology. PMID 33497606 DOI: 10.1016/j.chembiol.2021.01.003 |
0.691 |
|
| 2021 |
Mukherjee G, Nandekar PP, Wade RC. An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase. Communications Biology. 4: 55. PMID 33420418 DOI: 10.1038/s42003-020-01568-y |
0.791 |
|
| 2021 |
Aslam M, Kandasamy N, Ullah A, Paramasivam N, Öztürk MA, Naureen S, Arshad A, Badshah M, Khan K, Wajid M, Abbasi R, Ilyas M, Eils R, Schlesner M, Wade RC, et al. Putative second hit rare genetic variants in families with seemingly GBA-associated Parkinson's disease. Npj Genomic Medicine. 6: 2. PMID 33402667 DOI: 10.1038/s41525-020-00163-8 |
0.341 |
|
| 2020 |
Holderbach S, Adam L, Jayaram B, Wade RC, Mukherjee G. RASPD+: Fast Protein-Ligand Binding Free Energy Prediction Using Simplified Physicochemical Features. Frontiers in Molecular Biosciences. 7: 601065. PMID 33392260 DOI: 10.3389/fmolb.2020.601065 |
0.699 |
|
| 2020 |
Kokh DB, Doser B, Richter S, Ormersbach F, Cheng X, Wade RC. A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories. The Journal of Chemical Physics. 153: 125102. PMID 33003755 DOI: 10.1063/5.0019088 |
0.7 |
|
| 2020 |
Nunes-Alves A, Kokh DB, Wade RC. Recent progress in molecular simulation methods for drug binding kinetics. Current Opinion in Structural Biology. 64: 126-133. PMID 32771530 DOI: 10.1016/J.Sbi.2020.06.022 |
0.727 |
|
| 2020 |
Öztürk MA, Wade RC. Computation of FRAP recovery times for linker histone - chromatin binding on the basis of Brownian dynamics simulations. Biochimica Et Biophysica Acta. General Subjects. 1864: 129653. PMID 32512172 DOI: 10.1016/J.Bbagen.2020.129653 |
0.556 |
|
| 2020 |
Diestelkoetter-Bachert P, Beck R, Reckmann I, Hellwig A, Garcia-Saez A, Zelman-Hopf M, Hanke A, Nunes Alves A, Wade RC, Mayer MP, Wieland F. Structural characterization of an Arf dimer interface: molecular mechanism of Arf-dependent membrane scission. Febs Letters. PMID 32394429 DOI: 10.1002/1873-3468.13808 |
0.753 |
|
| 2020 |
Mustafa G, Nandekar PP, Mukherjee G, Bruce NJ, Wade RC. The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics. Scientific Reports. 10: 7284. PMID 32350331 DOI: 10.1038/S41598-020-64129-7 |
0.798 |
|
| 2020 |
Yuan JH, Han SB, Richter S, Wade RC, Kokh DB. Druggability Assessment in TRAPP using Machine Learning Approaches. Journal of Chemical Information and Modeling. PMID 32105476 DOI: 10.1021/Acs.Jcim.9B01185 |
0.737 |
|
| 2020 |
Moreau CA, Quadt KA, Piirainen H, Kumar H, Bhargav SP, Strauss L, Tolia NH, Wade RC, Spatz JP, Kursula I, Frischknecht F. A function of profilin in force generation during malaria parasite motility independent of actin binding. Journal of Cell Science. PMID 32034083 DOI: 10.1242/Jcs.233775 |
0.311 |
|
| 2020 |
Öztürk MA, De M, Cojocaru V, Wade RC. Chromatosome Structure and Dynamics from Molecular Simulations. Annual Review of Physical Chemistry. PMID 32017651 DOI: 10.1146/Annurev-Physchem-071119-040043 |
0.757 |
|
| 2019 |
Mereghetti P, Martinez M, Wade RC. Correction to: Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules. Bmc Biophysics. 12: 2. PMID 32181605 DOI: 10.1186/S13628-020-0026-Z |
0.756 |
|
| 2019 |
Bruce NJ, Narzi D, Trpevski D, van Keulen SC, Nair AG, Röthlisberger U, Wade RC, Carloni P, Hellgren Kotaleski J. Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals. Plos Computational Biology. 15: e1007382. PMID 31665146 DOI: 10.1371/Journal.Pcbi.1007382 |
0.607 |
|
| 2019 |
Mustafa G, Nandekar PP, Bruce NJ, Wade RC. Differing Membrane Interactions of Two Highly Similar Drug-Metabolizing Cytochrome P450 Isoforms: CYP 2C9 and CYP 2C19. International Journal of Molecular Sciences. 20. PMID 31487853 DOI: 10.3390/Ijms20184328 |
0.793 |
|
| 2019 |
Bruce NJ, Ganotra GK, Richter S, Wade RC. KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding. Journal of Chemical Information and Modeling. PMID 31381336 DOI: 10.1021/Acs.Jcim.9B00485 |
0.785 |
|
| 2019 |
Kokh DB, Kaufmann T, Kister B, Wade RC. Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times. Frontiers in Molecular Biosciences. 6: 36. PMID 31179286 DOI: 10.3389/Fmolb.2019.00036 |
0.735 |
|
| 2019 |
Tong R, Wade RC, Bruce NJ. Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties. Proteins. 87: 619-620. PMID 31152609 DOI: 10.1002/prot.25698 |
0.503 |
|
| 2019 |
Moraes CB, Witt G, Kuzikov M, Ellinger B, Calogeropoulou T, Prousis KC, Mangani S, Di Pisa F, Landi G, Iacono LD, Pozzi C, Freitas-Junior LH, Dos Santos Pascoalino B, Bertolacini CP, Behrens B, ... ... Wade RC, et al. Accelerating Drug Discovery Efforts for Trypanosomatidic Infections Using an Integrated Transnational Academic Drug Discovery Platform. Slas Discovery : Advancing Life Sciences R & D. 24: 346-361. PMID 30784368 DOI: 10.1177/2472555218823171 |
0.778 |
|
| 2019 |
Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, ... ... Wade RC, et al. Allostery in Its Many Disguises: From Theory to Applications. Structure (London, England : 1993). PMID 30744993 DOI: 10.1016/J.Str.2019.01.003 |
0.782 |
|
| 2019 |
Mustafa G, Nandekar PP, Camp TJ, Bruce NJ, Gregory MC, Sligar SG, Wade RC. Influence of Transmembrane Helix Mutations on Cytochrome P450-Membrane Interactions and Function. Biophysical Journal. PMID 30658838 DOI: 10.1016/J.Bpj.2018.12.014 |
0.794 |
|
| 2018 |
Ganotra GK, Wade RC. Prediction of Drug-Target Binding Kinetics by Comparative Binding Energy Analysis. Acs Medicinal Chemistry Letters. 9: 1134-1139. PMID 30429958 DOI: 10.1021/Acsmedchemlett.8B00397 |
0.811 |
|
| 2018 |
Douglas RG, Nandekar P, Aktories JE, Kumar H, Weber R, Sattler JM, Singer M, Lepper S, Sadiq SK, Wade RC, Frischknecht F. Inter-subunit interactions drive divergent dynamics in mammalian and Plasmodium actin filaments. Plos Biology. 16: e2005345. PMID 30011270 DOI: 10.1371/Journal.Pbio.2005345 |
0.709 |
|
| 2018 |
Öztürk MA, Cojocaru V, Wade RC. Toward an Ensemble View of Chromatosome Structure: A Paradigm Shift from One to Many. Structure (London, England : 1993). PMID 29937356 DOI: 10.1016/J.Str.2018.05.009 |
0.737 |
|
| 2018 |
Kokh DB, Amaral M, Bomke J, Grädler U, Musil D, Buchstaller HP, Dreyer MK, Frech M, Lowinski M, Vallee F, Bianciotto M, Rak A, Wade RC. Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 29768913 DOI: 10.1021/Acs.Jctc.8B00230 |
0.716 |
|
| 2018 |
Öztürk MA, Cojocaru V, Wade RC. Dependence of Chromatosome Structure on Linker Histone Sequence and Posttranslational Modification. Biophysical Journal. PMID 29759374 DOI: 10.1016/J.Bpj.2018.04.034 |
0.757 |
|
| 2018 |
Heroven C, Georgi V, Ganotra GK, Brennan PE, Wolfreys F, Wade RC, Fernández-Montalván AE, Chaikuad A, Knapp S. Halogen-aromatic π-interactions modulate inhibitor residence time. Angewandte Chemie (International Ed. in English). PMID 29601130 DOI: 10.1002/Anie.201801666 |
0.798 |
|
| 2018 |
Sadiq SK, Wade RC. Computing Protein-Ligand Binding Association Rate Constants by Combining Brownian Dynamics and Molecular Dynamics Simulations Biophysical Journal. 114: 56a. DOI: 10.1016/J.Bpj.2017.11.357 |
0.404 |
|
| 2018 |
Heroven C, Georgi V, Ganotra GK, Brennan P, Wolfreys F, Wade RC, Fernández-Montalván AE, Chaikuad A, Knapp S. Halogenaromatische π-Wechselwirkungen modulieren die Verweilzeit von Inhibitoren Angewandte Chemie. 130: 7338-7343. DOI: 10.1002/Ange.201801666 |
0.746 |
|
| 2017 |
Amaral M, Kokh DB, Bomke J, Wegener A, Buchstaller HP, Eggenweiler HM, Matias P, Sirrenberg C, Wade RC, Frech M. Protein conformational flexibility modulates kinetics and thermodynamics of drug binding. Nature Communications. 8: 2276. PMID 29273709 DOI: 10.1038/S41467-017-02258-W |
0.743 |
|
| 2017 |
Rafiullah R, Long AB, Ivanova AA, Ali H, Berkel S, Mustafa G, Paramasivam N, Schlesner M, Wiemann S, Wade RC, Bolthauser E, Blum M, Kahn RA, Caspary T, Rappold GA. A novel homozygous ARL13B variant in patients with Joubert syndrome impairs its guanine nucleotide-exchange factor activity. European Journal of Human Genetics : Ejhg. 25: 1324-1334. PMID 29255182 DOI: 10.1038/S41431-017-0031-0 |
0.502 |
|
| 2017 |
Bruce NJ, Ganotra GK, Kokh DB, Sadiq SK, Wade RC. New approaches for computing ligand-receptor binding kinetics. Current Opinion in Structural Biology. 49: 1-10. PMID 29132080 DOI: 10.1016/J.Sbi.2017.10.001 |
0.802 |
|
| 2017 |
Panecka-Hofman J, Pöhner I, Spyrakis F, Zeppelin T, Di Pisa F, Dello Iacono L, Bonucci A, Quotadamo A, Venturelli A, Mangani S, Costi MP, Wade RC. Comparative mapping of on-targets and off-targets for the discovery of anti-trypanosomatid folate pathway inhibitors. Biochimica Et Biophysica Acta. PMID 28939533 DOI: 10.1016/J.Bbagen.2017.09.012 |
0.778 |
|
| 2017 |
Jedwabny W, Panecka-Hofman J, Dyguda-Kazimierowicz E, Wade RC, Sokalski WA. Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition. Journal of Computer-Aided Molecular Design. PMID 28688090 DOI: 10.1007/S10822-017-0035-4 |
0.791 |
|
| 2017 |
Moreau CA, Bhargav SP, Kumar H, Quadt KA, Piirainen H, Strauss L, Kehrer J, Streichfuss M, Spatz JP, Wade RC, Kursula I, Frischknecht F. A unique profilin-actin interface is important for malaria parasite motility. Plos Pathogens. 13: e1006412. PMID 28552953 DOI: 10.1371/Journal.Ppat.1006412 |
0.335 |
|
| 2017 |
Nillegoda NB, Stank A, Malinverni D, Alberts N, Szlachcic A, Barducci A, De Los Rios P, Wade RC, Bukau B. Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes. Elife. 6. PMID 28504929 DOI: 10.7554/Elife.24560 |
0.343 |
|
| 2017 |
Stank A, Kokh DB, Horn M, Sizikova E, Neil R, Panecka J, Richter S, Wade RC. TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets. Nucleic Acids Research. PMID 28431137 DOI: 10.1093/Nar/Gkx277 |
0.734 |
|
| 2017 |
Schuetz DA, de Witte WEA, Wong YC, Knasmueller B, Richter L, Kokh DB, Sadiq SK, Bosma R, Nederpelt I, Segala E, Amaral M, Guo D, Andres D, Georgi V, Stoddart LA, ... ... Wade RC, et al. Kinetics for Drug Discovery: an industry-driven effort to target drug residence time. Drug Discovery Today. PMID 28412474 DOI: 10.1016/J.Drudis.2017.02.002 |
0.704 |
|
| 2017 |
Di Pisa F, Landi G, Dello Iacono L, Pozzi C, Borsari C, Ferrari S, Santucci M, Santarem N, Cordeiro-da-Silva A, Moraes CB, Alcantara LM, Fontana V, Freitas-Junior LH, Gul S, Kuzikov M, ... ... Wade RC, et al. Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity. Molecules (Basel, Switzerland). 22. PMID 28282886 DOI: 10.3390/Molecules22030426 |
0.312 |
|
| 2016 |
Tong R, Wade RC, Bruce NJ. Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties. Proteins. PMID 27667304 DOI: 10.1002/Prot.25167 |
0.611 |
|
| 2016 |
Schibich D, Gloge F, Pöhner I, Björkholm P, Wade RC, von Heijne G, Bukau B, Kramer G. Global profiling of SRP interaction with nascent polypeptides. Nature. PMID 27487212 DOI: 10.1038/Nature19070 |
0.381 |
|
| 2016 |
Ozboyaci M, Martinez M, Wade RC. An Efficient Low Storage and Memory Treatment of Gridded Interaction Fields for Simulations of Macromolecular Association. Journal of Chemical Theory and Computation. PMID 27463233 DOI: 10.1021/Acs.Jctc.6B00350 |
0.794 |
|
| 2016 |
Kokh DB, Czodrowski P, Rippmann F, Wade RC. Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets. Journal of Chemical Theory and Computation. PMID 27399277 DOI: 10.1021/Acs.Jctc.6B00101 |
0.736 |
|
| 2016 |
Öztürk MA, Pachov GV, Wade RC, Cojocaru V. Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome. Nucleic Acids Research. PMID 27270081 DOI: 10.1093/Nar/Gkw514 |
0.748 |
|
| 2016 |
Subramanian SR, Singam ER, Berinski M, Subramanian V, Wade RC. Identification of an Electrostatic Ruler Motif for Sequence-Specific Binding of Collagenase to Collagen. The Journal of Physical Chemistry. B. PMID 27245212 DOI: 10.1021/Acs.Jpcb.6B02573 |
0.314 |
|
| 2016 |
Wild K, Bange G, Motiejunas D, Kribelbauer J, Hendricks A, Segnitz B, Wade RC, Sinning I. Structural basis for conserved regulation and adaptation of the signal recognition particle targeting complex. Journal of Molecular Biology. PMID 27241309 DOI: 10.1016/J.Jmb.2016.05.015 |
0.334 |
|
| 2016 |
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, ... ... Wade RC, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007 |
0.702 |
|
| 2016 |
Stank A, Kokh DB, Fuller JC, Wade RC. Protein Binding Pocket Dynamics. Accounts of Chemical Research. 49: 809-15. PMID 27110726 DOI: 10.1021/Acs.Accounts.5B00516 |
0.739 |
|
| 2016 |
Ozboyaci M, Kokh DB, Wade RC. Three steps to gold: mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations. Physical Chemistry Chemical Physics : Pccp. 18: 10191-200. PMID 27021898 DOI: 10.1039/C6Cp00201C |
0.808 |
|
| 2016 |
Ozboyaci M, Kokh DB, Corni S, Wade RC. Modeling and simulation of protein-surface interactions: achievements and challenges. Quarterly Reviews of Biophysics. 49: e4. PMID 26821792 DOI: 10.1017/S0033583515000256 |
0.811 |
|
| 2016 |
Ozboyaci M, Kokh DB, Wade RC. Three steps to gold: Mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations Physical Chemistry Chemical Physics. 18: 10191-10200. DOI: 10.1039/c6cp00201c |
0.804 |
|
| 2016 |
Ozboyaci M, Kokh DB, Corni S, Wade RC. Modeling and simulation of protein-surface interactions: Achievements and challenges Quarterly Reviews of Biophysics. 49. DOI: 10.1017/S0033583515000256 |
0.796 |
|
| 2015 |
Mustafa G, Nandekar PP, Yu X, Wade RC. On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer. The Journal of Chemical Physics. 143: 243139. PMID 26723624 DOI: 10.1063/1.4936909 |
0.81 |
|
| 2015 |
Wang T, Wade RC. Force Field Effects on a β-Sheet Protein Domain Structure in Thermal Unfolding Simulations. Journal of Chemical Theory and Computation. 2: 140-8. PMID 26626388 DOI: 10.1021/Ct0501607 |
0.32 |
|
| 2015 |
Rafiullah R, Aslamkhan M, Paramasivam N, Thiel C, Mustafa G, Wiemann S, Schlesner M, Wade RC, Rappold GA, Berkel S. Homozygous missense mutation in the LMAN2L gene segregates with intellectual disability in a large consanguineous Pakistani family. Journal of Medical Genetics. PMID 26566883 DOI: 10.1136/Jmedgenet-2015-103179 |
0.472 |
|
| 2015 |
Yu X, Nandekar P, Mustafa G, Cojocaru V, Lepesheva GI, Wade RC. Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design. Biochimica Et Biophysica Acta. 1860: 67-78. PMID 26493722 DOI: 10.1016/J.Bbagen.2015.10.015 |
0.784 |
|
| 2015 |
Romanowska J, Kokh DB, Wade RC. When the Label Matters: Adsorption of Labeled and Unlabeled Proteins on Charged Surfaces. Nano Letters. 15: 7508-13. PMID 26491986 DOI: 10.1021/Acs.Nanolett.5B03168 |
0.792 |
|
| 2015 |
Tomić A, Berynskyy M, Wade RC, Tomić S. Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding. Molecular Biosystems. PMID 26334575 DOI: 10.1039/C5Mb00465A |
0.428 |
|
| 2015 |
Nillegoda NB, Kirstein J, Szlachcic A, Berynskyy M, Stank A, Stengel F, Arnsburg K, Gao X, Scior A, Aebersold R, Guilbride DL, Wade RC, Morimoto RI, Mayer MP, Bukau B. Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation. Nature. 524: 247-51. PMID 26245380 DOI: 10.1038/Nature14884 |
0.343 |
|
| 2015 |
Martinez M, Bruce NJ, Romanowska J, Kokh DB, Ozboyaci M, Yu X, Öztürk MA, Richter S, Wade RC. SDA 7: A modular and parallel implementation of the simulation of diffusional association software. Journal of Computational Chemistry. PMID 26123630 DOI: 10.1002/Jcc.23971 |
0.777 |
|
| 2015 |
Seybold C, Elserafy M, Rüthnick D, Ozboyaci M, Neuner A, Flottmann B, Heilemann M, Wade RC, Schiebel E. Kar1 binding to Sfi1 C-terminal regions anchors the SPB bridge to the nuclear envelope. The Journal of Cell Biology. 209: 843-61. PMID 26076691 DOI: 10.1083/Jcb.201412050 |
0.786 |
|
| 2015 |
Liu L, Wade RC, Heermann DW. A multiscale approach to simulating the conformational properties of unbound multi-C2 H2 zinc finger proteins. Proteins. 83: 1604-15. PMID 26062035 DOI: 10.1002/Prot.24845 |
0.399 |
|
| 2015 |
Yu X, Martinez M, Gable AL, Fuller JC, Bruce NJ, Richter S, Wade RC. webSDA: a web server to simulate macromolecular diffusional association. Nucleic Acids Research. 43: W220-4. PMID 25883142 DOI: 10.1093/Nar/Gkv335 |
0.775 |
|
| 2015 |
Salo-Ahen OM, Tochowicz A, Pozzi C, Cardinale D, Ferrari S, Boum Y, Mangani S, Stroud RM, Saxena P, Myllykallio H, Costi MP, Ponterini G, Wade RC. Hotspots in an obligate homodimeric anticancer target. Structural and functional effects of interfacial mutations in human thymidylate synthase. Journal of Medicinal Chemistry. 58: 3572-81. PMID 25798950 DOI: 10.1021/Acs.Jmedchem.5B00137 |
0.353 |
|
| 2015 |
Yu X, Cojocaru V, Mustafa G, Salo-Ahen OM, Lepesheva GI, Wade RC. Dynamics of CYP51: implications for function and inhibitor design. Journal of Molecular Recognition : Jmr. 28: 59-73. PMID 25601796 DOI: 10.1002/Jmr.2412 |
0.81 |
|
| 2015 |
Fuller JC, Martinez M, Henrich S, Stank A, Richter S, Wade RC. LigDig: a web server for querying ligand-protein interactions. Bioinformatics (Oxford, England). 31: 1147-9. PMID 25433696 DOI: 10.1093/Bioinformatics/Btu784 |
0.639 |
|
| 2014 |
Fuller JC, Martinez M, Wade RC. On calculation of the electrostatic potential of a phosphatidylinositol phosphate-containing phosphatidylcholine lipid membrane accounting for membrane dynamics. Plos One. 9: e104778. PMID 25141217 DOI: 10.1371/Journal.Pone.0104778 |
0.654 |
|
| 2014 |
Mereghetti P, Martinez M, Wade RC. Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules. Bmc Biophysics. 7: 4. PMID 25045516 DOI: 10.1186/2046-1682-7-4 |
0.792 |
|
| 2014 |
Wade RC, Henrich S, Wang T. Using 3D protein structures to derive 3D-QSARs. Drug Discovery Today. Technologies. 1: 241-6. PMID 24981491 DOI: 10.1016/J.Ddtec.2004.11.018 |
0.333 |
|
| 2013 |
Gombos L, Neuner A, Berynskyy M, Fava LL, Wade RC, Sachse C, Schiebel E. GTP regulates the microtubule nucleation activity of γ-tubulin. Nature Cell Biology. 15: 1317-27. PMID 24161932 DOI: 10.1038/Ncb2863 |
0.328 |
|
| 2013 |
Veith N, Feldman-Salit A, Cojocaru V, Henrich S, Kummer U, Wade RC. Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria. Plos Computational Biology. 9: e1003159. PMID 23946717 DOI: 10.1371/Journal.Pcbi.1003159 |
0.707 |
|
| 2013 |
Sandikci A, Gloge F, Martinez M, Mayer MP, Wade R, Bukau B, Kramer G. Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding. Nature Structural & Molecular Biology. 20: 843-50. PMID 23770820 DOI: 10.1038/Nsmb.2615 |
0.599 |
|
| 2013 |
Feldman-Salit A, Hering S, Messiha HL, Veith N, Cojocaru V, Sieg A, Westerhoff HV, Kreikemeyer B, Wade RC, Fiedler T. Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria. The Journal of Biological Chemistry. 288: 21295-306. PMID 23720742 DOI: 10.1074/Jbc.M113.458265 |
0.689 |
|
| 2013 |
Kokh DB, Richter S, Henrich S, Czodrowski P, Rippmann F, Wade RC. TRAPP: a tool for analysis of transient binding pockets in proteins. Journal of Chemical Information and Modeling. 53: 1235-52. PMID 23621586 DOI: 10.1021/Ci4000294 |
0.73 |
|
| 2013 |
Yu X, Cojocaru V, Wade RC. Conformational diversity and ligand tunnels of mammalian cytochrome P450s. Biotechnology and Applied Biochemistry. 60: 134-45. PMID 23587001 DOI: 10.1002/Bab.1074 |
0.783 |
|
| 2013 |
Balbo J, Mereghetti P, Herten DP, Wade RC. The shape of protein crowders is a major determinant of protein diffusion. Biophysical Journal. 104: 1576-84. PMID 23561534 DOI: 10.1016/J.Bpj.2013.02.041 |
0.736 |
|
| 2013 |
Wade RC. Targeting protein dynamics in drug design Journal of Cheminformatics. 5. DOI: 10.1186/1758-2946-5-S1-O1 |
0.394 |
|
| 2012 |
Brancolini G, Kokh DB, Calzolai L, Wade RC, Corni S. Docking of ubiquitin to gold nanoparticles. Acs Nano. 6: 9863-78. PMID 23033917 DOI: 10.1021/Nn303444B |
0.69 |
|
| 2012 |
Mereghetti P, Wade RC. Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions. The Journal of Physical Chemistry. B. 116: 8523-33. PMID 22594708 DOI: 10.1021/Jp212532H |
0.741 |
|
| 2012 |
Stein M, Pilli M, Bernauer S, Habermann BH, Zerial M, Wade RC. The interaction properties of the human Rab GTPase family--comparative analysis reveals determinants of molecular binding selectivity. Plos One. 7: e34870. PMID 22523562 DOI: 10.1371/Journal.Pone.0034870 |
0.644 |
|
| 2012 |
Feldman-Salit A, Wirtz M, Lenherr ED, Throm C, Hothorn M, Scheffzek K, Hell R, Wade RC. Allosterically gated enzyme dynamics in the cysteine synthase complex regulate cysteine biosynthesis in Arabidopsis thaliana. Structure (London, England : 1993). 20: 292-302. PMID 22325778 DOI: 10.1016/J.Str.2011.11.019 |
0.307 |
|
| 2012 |
Cojocaru V, Winn PJ, Wade RC. Multiple, ligand-dependent routes from the active site of cytochrome P450 2C9. Current Drug Metabolism. 13: 143-54. PMID 22208529 DOI: 10.2174/138920012798918462 |
0.741 |
|
| 2011 |
Salo-Ahen OM, Wade RC. The active-inactive transition of human thymidylate synthase: targeted molecular dynamics simulations. Proteins. 79: 2886-99. PMID 21905113 DOI: 10.1002/Prot.23123 |
0.311 |
|
| 2011 |
Cojocaru V, Balali-Mood K, Sansom MS, Wade RC. Structure and dynamics of the membrane-bound cytochrome P450 2C9. Plos Computational Biology. 7: e1002152. PMID 21852944 DOI: 10.1371/Journal.Pcbi.1002152 |
0.732 |
|
| 2011 |
Cardinale D, Guaitoli G, Tondi D, Luciani R, Henrich S, Salo-Ahen OM, Ferrari S, Marverti G, Guerrieri D, Ligabue A, Frassineti C, Pozzi C, Mangani S, Fessas D, Guerrini R, ... ... Wade RC, et al. Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase. Proceedings of the National Academy of Sciences of the United States of America. 108: E542-9. PMID 21795601 DOI: 10.1073/Pnas.1104829108 |
0.351 |
|
| 2011 |
Mereghetti P, Kokh D, McCammon JA, Wade RC. Diffusion and association processes in biological systems: theory, computation and experiment. Bmc Biophysics. 4: 2. PMID 21595997 DOI: 10.1186/2046-1682-4-2 |
0.772 |
|
| 2011 |
Mereghetti P, Wade RC. Diffusion of hydrophobin proteins in solution and interactions with a graphite surface. Bmc Biophysics. 4: 9. PMID 21595866 DOI: 10.1186/2046-1682-4-9 |
0.73 |
|
| 2011 |
Cohavi O, Reichmann D, Abramovich R, Tesler AB, Bellapadrona G, Kokh DB, Wade RC, Vaskevich A, Rubinstein I, Schreiber G. A quantitative, real-time assessment of binding of peptides and proteins to gold surfaces. Chemistry (Weinheim An Der Bergstrasse, Germany). 17: 1327-36. PMID 21243701 DOI: 10.1002/Chem.201001781 |
0.718 |
|
| 2011 |
Ferrari S, Morandi F, Motiejunas D, Nerini E, Henrich S, Luciani R, Venturelli A, Lazzari S, Calò S, Gupta S, Hannaert V, Michels PA, Wade RC, Costi MP. Virtual screening identification of nonfolate compounds, including a CNS drug, as antiparasitic agents inhibiting pteridine reductase. Journal of Medicinal Chemistry. 54: 211-21. PMID 21126022 DOI: 10.1021/Jm1010572 |
0.31 |
|
| 2011 |
Cardinale D, Guaitoli G, Tondi D, Luciani R, Henrich S, Salo-Ahen OMH, Ferrari S, Marverti G, Guerrieri D, Ligabue A, Frassineti C, Pozzi C, Mangani S, Fessas D, Guerrini R, ... ... Wade RC, et al. Erratum: Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase (Proceedings of the National Academy of Sciences of the United States of America (2011) 108, 34 (E542-E549) DOI: 10.1073/pnas.1104829108) Proceedings of the National Academy of Sciences of the United States of America. 108: 16133-16133. DOI: 10.1073/Pnas.1113637108 |
0.302 |
|
| 2011 |
Kokh DB, Wade RC, Wenzel W. Receptor flexibility in small‐molecule docking calculations Wires Computational Molecular Science. 1: 298-314. DOI: 10.1002/Wcms.29 |
0.72 |
|
| 2010 |
Kokh DB, Corni S, Winn PJ, Hoefling M, Gottschalk KE, Wade RC. ProMetCS: An Atomistic Force Field for Modeling Protein-Metal Surface Interactions in a Continuum Aqueous Solvent. Journal of Chemical Theory and Computation. 6: 1753-68. PMID 26615704 DOI: 10.1021/Ct100086J |
0.726 |
|
| 2010 |
Mereghetti P, Gabdoulline RR, Wade RC. Brownian dynamics simulation of protein solutions: structural and dynamical properties. Biophysical Journal. 99: 3782-91. PMID 21112303 DOI: 10.1016/J.Bpj.2010.10.035 |
0.753 |
|
| 2010 |
Cardinale D, Salo-Ahen OM, Ferrari S, Ponterini G, Cruciani G, Carosati E, Tochowicz AM, Mangani S, Wade RC, Costi MP. Homodimeric enzymes as drug targets. Current Medicinal Chemistry. 17: 826-46. PMID 20156173 DOI: 10.2174/092986710790712156 |
0.42 |
|
| 2010 |
Stein M, Gabdoulline RR, Wade RC. Cross-species analysis of the glycolytic pathway by comparison of molecular interaction fields. Molecular Biosystems. 6: 152-64. PMID 20024078 DOI: 10.1039/B912398A |
0.613 |
|
| 2010 |
Cardinale D, Salo-Ahen OM, Guaitoli G, Ferrari S, Venturelli A, Franchini S, Battini R, Ponterini G, Wade RC, Costi MP. Design and characterization of a mutation outside the active site of human thymidylate synthase that affects ligand binding. Protein Engineering, Design & Selection : Peds. 23: 81-9. PMID 19955218 DOI: 10.1093/Protein/Gzp075 |
0.309 |
|
| 2010 |
Cohavi O, Corni S, De Rienzo F, Di Felice R, Gottschalk KE, Hoefling M, Kokh D, Molinari E, Schreiber G, Vaskevich A, Wade RC. Protein-surface interactions: challenging experiments and computations. Journal of Molecular Recognition : Jmr. 23: 259-62. PMID 19950121 DOI: 10.1002/Jmr.993 |
0.707 |
|
| 2010 |
Henrich S, Feierberg I, Wang T, Blomberg N, Wade RC. Comparative binding energy analysis for binding affinity and target selectivity prediction. Proteins. 78: 135-53. PMID 19768680 DOI: 10.1002/Prot.22579 |
0.386 |
|
| 2010 |
Henrich S, Salo-Ahen OM, Huang B, Rippmann FF, Cruciani G, Wade RC. Computational approaches to identifying and characterizing protein binding sites for ligand design. Journal of Molecular Recognition : Jmr. 23: 209-19. PMID 19746440 DOI: 10.1002/Jmr.984 |
0.448 |
|
| 2010 |
Kokh DB, Corni S, Winn PJ, Hoefling M, Gottschalk KE, Wade RC. ProMetCS: An atomistic force field for modeling protein-metal surface interactions in a continuum aqueous solvent Journal of Chemical Theory and Computation. 6: 1753-1768. DOI: 10.1021/ct100086j |
0.662 |
|
| 2009 |
Pavlova M, Klvana M, Prokop Z, Chaloupkova R, Banas P, Otyepka M, Wade RC, Tsuda M, Nagata Y, Damborsky J. Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nature Chemical Biology. 5: 727-33. PMID 19701186 DOI: 10.1038/Nchembio.205 |
0.315 |
|
| 2009 |
Klvana M, Pavlova M, Koudelakova T, Chaloupkova R, Dvorak P, Prokop Z, Stsiapanava A, Kuty M, Kuta-Smatanova I, Dohnalek J, Kulhanek P, Wade RC, Damborsky J. Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations. Journal of Molecular Biology. 392: 1339-56. PMID 19577578 DOI: 10.1016/J.Jmb.2009.06.076 |
0.329 |
|
| 2009 |
Gabdoulline RR, Wade RC. On the contributions of diffusion and thermal activation to electron transfer between Phormidium laminosum plastocyanin and cytochrome f: Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events. Journal of the American Chemical Society. 131: 9230-8. PMID 19518050 DOI: 10.1021/Ja809567K |
0.363 |
|
| 2009 |
Feldman-Salit A, Wirtz M, Hell R, Wade RC. A mechanistic model of the cysteine synthase complex. Journal of Molecular Biology. 386: 37-59. PMID 18801369 DOI: 10.1016/J.Jmb.2008.08.075 |
0.344 |
|
| 2009 |
Pachov GV, Wade RC. Docking of a Linker Histone to The Nucleosome With Flexible Linker DNAs Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.335 |
0.311 |
|
| 2009 |
Kokh DB, Huang B, Wade RC, Winn PJ. Modeling of Protein Adsorption on a Metal Surface: Brownian Dynamics Simulations Biophysical Journal. 96: 298a-299a. DOI: 10.1016/J.Bpj.2008.12.1483 |
0.413 |
|
| 2008 |
Weidemann A, Richter S, Stein M, Sahle S, Gauges R, Gabdoulline R, Surovtsova I, Semmelrock N, Besson B, Rojas I, Wade R, Kummer U. SYCAMORE--a systems biology computational analysis and modeling research environment. Bioinformatics (Oxford, England). 24: 1463-4. PMID 18463116 DOI: 10.1093/Bioinformatics/Btn207 |
0.603 |
|
| 2008 |
Richter S, Wenzel A, Stein M, Gabdoulline RR, Wade RC. webPIPSA: a web server for the comparison of protein interaction properties. Nucleic Acids Research. 36: W276-80. PMID 18420653 DOI: 10.1093/Nar/Gkn181 |
0.65 |
|
| 2008 |
Stein M, Gabdoulline RR, Wade RC. Calculating enzyme kinetic parameters from protein structures. Biochemical Society Transactions. 36: 51-4. PMID 18208384 DOI: 10.1042/Bst0360051 |
0.603 |
|
| 2008 |
Motiejunas D, Gabdoulline R, Wang T, Feldman-Salit A, Johann T, Winn PJ, Wade RC. Protein-protein docking by simulating the process of association subject to biochemical constraints. Proteins. 71: 1955-69. PMID 18186463 DOI: 10.1002/Prot.21867 |
0.393 |
|
| 2008 |
Bertosa B, Kojić-Prodić B, Wade RC, Tomić S. Mechanism of auxin interaction with Auxin Binding Protein (ABP1): a molecular dynamics simulation study. Biophysical Journal. 94: 27-37. PMID 17766341 DOI: 10.1529/Biophysj.107.109025 |
0.403 |
|
| 2007 |
Wang T, Wade RC. On the Use of Elevated Temperature in Simulations To Study Protein Unfolding Mechanisms. Journal of Chemical Theory and Computation. 3: 1476-83. PMID 26633218 DOI: 10.1021/Ct700063C |
0.335 |
|
| 2007 |
Gabdoulline RR, Stein M, Wade RC. qPIPSA: relating enzymatic kinetic parameters and interaction fields. Bmc Bioinformatics. 8: 373. PMID 17919319 DOI: 10.1186/1471-2105-8-373 |
0.609 |
|
| 2007 |
Winn PJ, Zahran M, Battey JN, Zhou Y, Wade RC, Banerjee A. Structural and electrostatic properties of ubiquitination and related pathways. Frontiers in Bioscience : a Journal and Virtual Library. 12: 3419-30. PMID 17485310 DOI: 10.2741/2323 |
0.347 |
|
| 2007 |
Stein M, Gabdoulline RR, Wade RC. Bridging from molecular simulation to biochemical networks. Current Opinion in Structural Biology. 17: 166-72. PMID 17395455 DOI: 10.1016/J.Sbi.2007.03.014 |
0.646 |
|
| 2007 |
Karyakin A, Motiejunas D, Wade RC, Jung C. FTIR studies of the redox partner interaction in cytochrome P450: the Pdx-P450cam couple. Biochimica Et Biophysica Acta. 1770: 420-31. PMID 17014964 DOI: 10.1016/J.Bbagen.2006.08.020 |
0.356 |
|
| 2007 |
Cojocaru V, Winn PJ, Wade RC. The ins and outs of cytochrome P450s. Biochimica Et Biophysica Acta. 1770: 390-401. PMID 16920266 DOI: 10.1016/J.Bbagen.2006.07.005 |
0.702 |
|
| 2006 |
Gabdoulline RR, Ulbrich S, Richter S, Wade RC. ProSAT2--Protein Structure Annotation Server. Nucleic Acids Research. 34: W79-83. PMID 16845114 DOI: 10.1093/Nar/Gkl216 |
0.332 |
|
| 2006 |
Hallingbäck HR, Gabdoulline RR, Wade RC. Comparison of the binding and reactivity of plant and mammalian peroxidases to indole derivatives by computational docking. Biochemistry. 45: 2940-50. PMID 16503648 DOI: 10.1021/Bi051510E |
0.351 |
|
| 2005 |
Spaar A, Dammer C, Gabdoulline RR, Wade RC, Helms V. Diffusional encounter of barnase and barstar. Biophysical Journal. 90: 1913-24. PMID 16361332 DOI: 10.1529/Biophysj.105.075507 |
0.365 |
|
| 2005 |
Wade RC, Motiejunas D, Schleinkofer K, Sudarko, Winn PJ, Banerjee A, Kariakin A, Jung C. Multiple molecular recognition mechanisms. Cytochrome P450--a case study. Biochimica Et Biophysica Acta. 1754: 239-44. PMID 16226496 DOI: 10.1016/J.Bbapap.2005.07.044 |
0.413 |
|
| 2005 |
Schleinkofer K, Sudarko, Winn PJ, Lüdemann SK, Wade RC. Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling? Embo Reports. 6: 584-9. PMID 16028306 DOI: 10.1038/Sj.Embor.7400420 |
0.328 |
|
| 2005 |
Kmunícek J, Hynková K, Jedlicka T, Nagata Y, Negri A, Gago F, Wade RC, Damborský J. Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26. Biochemistry. 44: 3390-401. PMID 15736949 DOI: 10.1021/Bi047912O |
0.39 |
|
| 2005 |
Ehrlich LP, Nilges M, Wade RC. The impact of protein flexibility on protein-protein docking Proteins: Structure, Function and Genetics. 58: 126-133. PMID 15515181 DOI: 10.1002/Prot.20272 |
0.41 |
|
| 2005 |
Wang T, Tomic S, Gabdoulline RR, Wade RC. How optimal are the binding energetics of barnase and barstar? Biophysical Journal. 87: 1618-30. PMID 15345541 DOI: 10.1529/Biophysj.104.040964 |
0.395 |
|
| 2005 |
McCammon JA, Wade RC. Theory and simulation: Pushing the limits Current Opinion in Structural Biology. 15: 135-136. DOI: 10.1016/J.Sbi.2005.03.009 |
0.411 |
|
| 2004 |
Schleinkofer K, Wiedemann U, Otte L, Wang T, Krause G, Oschkinat H, Wade RC. Comparative structural and energetic analysis of WW domain-peptide interactions. Journal of Molecular Biology. 344: 865-81. PMID 15533451 DOI: 10.1016/J.Jmb.2004.09.063 |
0.336 |
|
| 2004 |
Winn PJ, Religa TL, Battey JN, Banerjee A, Wade RC. Determinants of functionality in the ubiquitin conjugating enzyme family. Structure (London, England : 1993). 12: 1563-74. PMID 15341722 DOI: 10.1016/J.Str.2004.06.017 |
0.303 |
|
| 2004 |
Wade RC, Winn PJ, Schlichting I, Sudarko. A survey of active site access channels in cytochromes P450. Journal of Inorganic Biochemistry. 98: 1175-82. PMID 15219983 DOI: 10.1016/J.Jinorgbio.2004.02.007 |
0.348 |
|
| 2004 |
Rienzo FD, Gabdoulline RR, Wade RC, Sola M, Menziani MC. Computational approaches to structural and functional analysis of plastocyanin and other blue copper proteins. Cellular and Molecular Life Sciences. 61: 1123-1142. PMID 15141299 DOI: 10.1007/S00018-004-3181-5 |
0.374 |
|
| 2004 |
Ferrari S, Costi PM, Wade RC. Inhibitor specificity via protein dynamics: insights from the design of antibacterial agents targeted against thymidylate synthase. Chemistry & Biology. 10: 1183-93. PMID 14700626 DOI: 10.1016/J.Chembiol.2003.11.012 |
0.379 |
|
| 2004 |
Kmunícek J, Bohác M, Luengo S, Gago F, Wade RC, Damborský J. Comparative binding energy analysis of haloalkane dehalogenase substrates: modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations. Journal of Computer-Aided Molecular Design. 17: 299-311. PMID 14635723 DOI: 10.1023/A:1026159215220 |
0.372 |
|
| 2004 |
Bertosa B, Kojić-Prodić B, Wade RC, Ramek M, Piperaki S, Tsantili-Kakoulidou A, Tomić S. A new approach to predict the biological activity of molecules based on similarity of their interaction fields and the logP and logD values: application to auxins. Journal of Chemical Information and Computer Sciences. 43: 1532-41. PMID 14502487 DOI: 10.1021/Ci034063N |
0.346 |
|
| 2004 |
Gabdoulline RR, Kummer U, Olsen LF, Wade RC. Concerted simulations reveal how peroxidase compound III formation results in cellular oscillations. Biophysical Journal. 85: 1421-8. PMID 12944259 DOI: 10.1016/S0006-3495(03)74574-3 |
0.374 |
|
| 2003 |
Gabdoulline RR, Hoffmann R, Leitner F, Wade RC. ProSAT: functional annotation of protein 3D structures. Bioinformatics (Oxford, England). 19: 1723-5. PMID 15593408 DOI: 10.1093/Bioinformatics/Btg220 |
0.331 |
|
| 2003 |
Gabdoulline RR, Wade RC, Walther D. MolSurfer: A macromolecular interface navigator. Nucleic Acids Research. 31: 3349-51. PMID 12824324 DOI: 10.1093/Nar/Gkg588 |
0.357 |
|
| 2002 |
Wang T, Wade RC. Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation. Proteins. 50: 158-69. PMID 12471608 DOI: 10.1002/Prot.10248 |
0.403 |
|
| 2002 |
Wang T, Wade RC. Comparative binding energy (COMBINE) analysis of OppA-peptide complexes to relate structure to binding thermodynamics. Journal of Medicinal Chemistry. 45: 4828-37. PMID 12383008 DOI: 10.1021/Jm020900L |
0.366 |
|
| 2002 |
Winn PJ, Lüdemann SK, Gauges R, Lounnas V, Wade RC. Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a novel functional role for a buried arginine. Proceedings of the National Academy of Sciences of the United States of America. 99: 5361-6. PMID 11959989 DOI: 10.1073/Pnas.082522999 |
0.365 |
|
| 2002 |
Gabdoulline RR, Wade RC. Biomolecular diffusional association. Current Opinion in Structural Biology. 12: 204-13. PMID 11959498 DOI: 10.1016/S0959-440X(02)00311-1 |
0.408 |
|
| 2002 |
Banerjee A, Wade RC. Elusive recognition determinants for ubiquitination. Journal of Molecular Recognition : Jmr. 15: 3-5. PMID 11870916 DOI: 10.1002/Jmr.561 |
0.305 |
|
| 2002 |
De Rienzo F, Gabdoulline RR, Menziani MC, De Benedetti PG, Wade RC. Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f. Biophysical Journal. 81: 3090-104. PMID 11720977 DOI: 10.1016/S0006-3495(01)75947-4 |
0.334 |
|
| 2002 |
Wade RC, Ortiz AR, Gago F. Comparative Binding Energy Analysis Perspectives in Drug Discovery and Design. 19-34. DOI: 10.1023/A:1027247618908 |
0.401 |
|
| 2001 |
Kmunícek J, Luengo S, Gago F, Ortiz AR, Wade RC, Damborský J. Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. Biochemistry. 40: 8905-17. PMID 11467952 DOI: 10.1021/Bi010464P |
0.352 |
|
| 2001 |
Wang T, Wade RC. Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes. Journal of Medicinal Chemistry. 44: 961-71. PMID 11300878 DOI: 10.1021/Jm001070J |
0.37 |
|
| 2001 |
Gabdoulline RR, Wade RC. Protein-protein association: investigation of factors influencing association rates by brownian dynamics simulations. Journal of Molecular Biology. 306: 1139-55. PMID 11237623 DOI: 10.1006/Jmbi.2000.4404 |
0.381 |
|
| 2001 |
Das B, Helms V, Lounnas V, Wade RC. Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation data for camphor enantiomers bound to cytochrome P-450cam. Journal of Inorganic Biochemistry. 81: 121-31. PMID 11051557 DOI: 10.1016/S0162-0134(00)00095-7 |
0.367 |
|
| 2001 |
Nardi F, Kemmink J, Sattler M, Wade RC. The cisproline(i - 1)-aromatic(i) interaction: folding of the Ala-cisPro-Tyr peptide characterized by NMR and theoretical approaches. Journal of Biomolecular Nmr. 17: 63-77. PMID 10909867 DOI: 10.1023/A:1008380807603 |
0.35 |
|
| 2001 |
Wade RC, Gabdoulline RR, Rienzo FD. Protein interaction property similarity analysis International Journal of Quantum Chemistry. 83: 122-127. DOI: 10.1002/Qua.1204 |
0.393 |
|
| 2000 |
Lüdemann SK, Lounnas V, Wade RC. How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways. Journal of Molecular Biology. 303: 813-30. PMID 11061977 DOI: 10.1006/Jmbi.2000.4155 |
0.316 |
|
| 2000 |
Lüdemann SK, Lounnas V, Wade RC. How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms. Journal of Molecular Biology. 303: 797-811. PMID 11061976 DOI: 10.1006/Jmbi.2000.4154 |
0.369 |
|
| 2000 |
De Rienzo F, Gabdoulline RR, Menziani MC, Wade RC. Blue copper proteins: a comparative analysis of their molecular interaction properties. Protein Science : a Publication of the Protein Society. 9: 1439-54. PMID 10975566 DOI: 10.1110/Ps.9.8.1439 |
0.401 |
|
| 2000 |
Tomic S, Nilsson L, Wade RC. Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis Journal of Medicinal Chemistry. 43: 1780-1792. PMID 10794695 DOI: 10.1021/Jm9911175 |
0.357 |
|
| 2000 |
Gabdoulline RR, Wade RC. On the protein-protein diffusional encounter complex. Journal of Molecular Recognition : Jmr. 12: 226-34. PMID 10440993 DOI: 10.1002/(Sici)1099-1352(199907/08)12:4<226::Aid-Jmr462>3.0.Co;2-P |
0.354 |
|
| 1999 |
Blomberg N, Gabdoulline RR, Nilges M, Wade RC. Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity Proteins: Structure, Function and Genetics. 37: 379-387. PMID 10591098 DOI: 10.1002/(Sici)1097-0134(19991115)37:3<379::Aid-Prot6>3.0.Co;2-K |
0.381 |
|
| 1999 |
Ibragimova GT, Wade RC. Stability of the beta-sheet of the WW domain: A molecular dynamics simulation study. Biophysical Journal. 77: 2191-8. PMID 10512838 DOI: 10.1016/S0006-3495(99)77059-1 |
0.301 |
|
| 1999 |
Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC. Improving macromolecular electrostatics calculations. Protein Engineering. 12: 657-62. PMID 10469826 DOI: 10.1093/Protein/12.8.657 |
0.452 |
|
| 1999 |
Elcock AH, Gabdoulline RR, Wade RC, McCammon JA. Computer simulation of protein-protein association kinetics: Acetylcholinesterase-fasciculin Journal of Molecular Biology. 291: 149-162. PMID 10438612 DOI: 10.1006/Jmbi.1999.2919 |
0.548 |
|
| 1999 |
Lounnas V, Lüdemann SK, Wade RC. Towards molecular dynamics simulation of large proteins with a hydration shell at constant pressure. Biophysical Chemistry. 78: 157-82. PMID 10343386 DOI: 10.1016/S0301-4622(98)00237-3 |
0.398 |
|
| 1999 |
Bitomsky W, Wade RC. Docking of Glycosaminoglycans to Heparin-Binding Proteins: Validation for aFGF, bFGF, and Antithrombin and Application to IL-8 Journal of the American Chemical Society. 121: 3004-3013. DOI: 10.1021/Ja983319G |
0.38 |
|
| 1999 |
Knapp-Mohammady M, Jalkanen K, Nardi F, Wade R, Suhai S. L-Alanyl-L-alanine in the zwitterionic state: structures determined in the presence of explicit water molecules and with continuum models using density functional theory Chemical Physics. 240: 63-77. DOI: 10.1016/S0301-0104(98)00387-5 |
0.305 |
|
| 1998 |
Ringrose L, Lounnas V, Ehrlich L, Buchholz F, Wade R, Stewart AF. Comparative kinetic analysis of FLP and cre recombinases: mathematical models for DNA binding and recombination. Journal of Molecular Biology. 284: 363-384. PMID 9813124 DOI: 10.1006/Jmbi.1998.2149 |
0.336 |
|
| 1998 |
Helms V, Wade RC. Hydration energy landscape of the active site cavity in cytochrome P450cam. Proteins. 32: 381-96. PMID 9715913 DOI: 10.1002/(Sici)1097-0134(19980815)32:3<381::Aid-Prot12>3.0.Co;2-5 |
0.41 |
|
| 1998 |
Ibragimova GT, Wade RC. Importance of explicit salt ions for protein stability in molecular dynamics simulation. Biophysical Journal. 74: 2906-11. PMID 9635744 DOI: 10.1016/S0006-3495(98)77997-4 |
0.392 |
|
| 1998 |
Wade RC, Gabdoulline RR, Luty BA. Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases. Proteins. 31: 406-16. PMID 9626700 DOI: 10.1002/(Sici)1097-0134(19980601)31:4<406::Aid-Prot7>3.0.Co;2-F |
0.352 |
|
| 1998 |
Wade RC, Gabdoulline RR, Lüdemann SK, Lounnas V. Electrostatic steering and ionic tethering in enzyme-ligand binding: insights from simulations. Proceedings of the National Academy of Sciences of the United States of America. 95: 5942-9. PMID 9600896 DOI: 10.1073/Pnas.95.11.5942 |
0.388 |
|
| 1998 |
Gabdoulline RR, Wade RC. Brownian dynamics simulation of protein-protein diffusional encounter. Methods (San Diego, Calif.). 14: 329-41. PMID 9571088 DOI: 10.1006/Meth.1998.0588 |
0.406 |
|
| 1998 |
Tomić S, Gabdoulline RR, Kojić-Prodić B, Wade RC. Classification of auxin plant hormones by interaction property similarity indices. Journal of Computer-Aided Molecular Design. 12: 63-79. PMID 9570090 DOI: 10.1023/A:1007973008558 |
0.308 |
|
| 1998 |
Worth GA, and FN, Wade RC. Use of Multiple Molecular Dynamics Trajectories To Study Biomolecules in Solution: The YTGP Peptide Journal of Physical Chemistry B. 102: 6260-6272. DOI: 10.1021/Jp9808532 |
0.326 |
|
| 1998 |
Helms V, Wade RC. Computational Alchemy To Calculate Absolute Protein−Ligand Binding Free Energy Journal of the American Chemical Society. 120: 2710-2713. DOI: 10.1021/Ja9738539 |
0.407 |
|
| 1997 |
Sobolev V, Moallem TM, Wade RC, Vriend G, Edelman M. CASP2 molecular docking predictions with the LIGIN software Proteins: Structure, Function and Genetics. 29: 210-214. PMID 9485514 DOI: 10.1002/(Sici)1097-0134(1997)1+<210::Aid-Prot28>3.0.Co;2-Q |
0.384 |
|
| 1997 |
Nardi F, Worth GA, Wade RC. Local interactions of aromatic residues in short peptides in aqueous solution: a combined database and energetic analysis. Folding & Design. 2: S62-8. PMID 9269571 DOI: 10.1016/S1359-0278(97)00066-7 |
0.315 |
|
| 1997 |
Gabdoulline RR, Wade RC. Analytically defined surfaces to analyze molecular interaction properties. Journal of Molecular Graphics. 14: 341-53, 374-5. PMID 9195487 DOI: 10.1016/S0263-7855(97)00008-8 |
0.313 |
|
| 1997 |
Lounnas V, Wade RC. Exceptionally stable salt bridges in cytochrome P450cam have functional roles. Biochemistry. 36: 5402-17. PMID 9154922 DOI: 10.1021/Bi9622940 |
0.37 |
|
| 1997 |
Gabdoulline RR, Wade RC. Simulation of the diffusional association of barnase and barstar. Biophysical Journal. 72: 1917-29. PMID 9129797 DOI: 10.1016/S0006-3495(97)78838-6 |
0.381 |
|
| 1997 |
Ortiz AR, Pastor M, Palomer A, Cruciani G, Gago F, Wade RC. Reliability of comparative molecular field analysis models: effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors. Journal of Medicinal Chemistry. 40: 1136-48. PMID 9089335 DOI: 10.1021/Jm9601617 |
0.323 |
|
| 1997 |
Worth GA, Lecuyer C, Wade RC. TRAJAN: a tool for analyzing trajectories from molecular simulations. Journal of Molecular Graphics. 14: 173-82, 146-7. PMID 8901645 DOI: 10.1016/S0263-7855(96)00059-8 |
0.309 |
|
| 1997 |
Ortiz AR, Pastor M, Palomer A, Cruciani G, Gago F, Wade RC, Pisabarro MT. Reliability of CoMFA Models: Effects of Data Scaling and Variable Selection using a Set of Human Synovial Fluid Phospholipase A2InhibitorsPrediction of Drug Binding Affinities by Comparative Binding Energy Analysis Journal of Medicinal Chemistry. 40: 4168-4168. DOI: 10.1021/Jm970629L |
0.327 |
|
| 1997 |
Lüdemann SK, Carugo O, Wade RC. Substrate Access to Cytochrome P450cam: A Comparison of a Thermal Motion Pathway Analysis with Molecular Dynamics Simulation Data Journal of Molecular Modeling. 3: 369-374. DOI: 10.1007/S008940050053 |
0.317 |
|
| 1997 |
Helms V, Wade RC. Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy Journal of Computational Chemistry. 18: 449-462. DOI: 10.1002/(Sici)1096-987X(199703)18:4<449::Aid-Jcc1>3.0.Co;2-T |
0.325 |
|
| 1996 |
Schulze H, Hoa GH, Helms V, Wade RC, Jung C. Structural changes in cytochrome P-450cam effected by the binding of the enantiomers (1R)-camphor and (1S)-camphor. Biochemistry. 35: 14127-38. PMID 8916898 DOI: 10.1021/Bi9527303 |
0.307 |
|
| 1996 |
Peters GH, Olsen OH, Svendsen A, Wade RC. Theoretical investigation of the dynamics of the active site lid in Rhizomucor miehei lipase. Biophysical Journal. 71: 119-29. PMID 8804595 DOI: 10.1016/S0006-3495(96)79207-X |
0.341 |
|
| 1996 |
Sobolev V, Wade RC, Vriend G, Edelman M. Molecular docking using surface complementarity Proteins: Structure, Function and Genetics. 25: 120-129. PMID 8727324 DOI: 10.1002/(Sici)1097-0134(199605)25:1<120::Aid-Prot10>3.0.Co;2-M |
0.373 |
|
| 1996 |
Helms V, Wade RC. Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study. Biophysical Journal. 69: 810-24. PMID 8519982 DOI: 10.1016/S0006-3495(95)79955-6 |
0.377 |
|
| 1996 |
Demchuk E, Wade RC. Improving the Continuum Dielectric Approach to Calculating pKas of Ionizable Groups in Proteins The Journal of Physical Chemistry. 100: 17373-17387. DOI: 10.1021/Jp960111D |
0.361 |
|
| 1995 |
Pisabarro MT, Ortiz AR, Serrano L, Wade RC. Homology modeling of the Abl-SH3 domain. Proteins. 20: 203-15. PMID 7892170 DOI: 10.1002/Prot.340200302 |
0.365 |
|
| 1995 |
Wade RC. Simulation of enzyme-substrate interactions: the diffusional encounter step. Acta Biochimica Polonica. 42: 419-425. DOI: 10.18388/Abp.1995_4895 |
0.351 |
|
| 1994 |
Wade RC, Luty BA, Demchuk E, Madura JD, Davis ME, Briggs JM, McCammon JA. Simulation of enzyme-substrate encounter with gated active sites. Nature Structural Biology. 1: 65-9. PMID 7656010 DOI: 10.1038/Nsb0194-65 |
0.741 |
|
| 1993 |
Wade RC, Davis ME, Luty BA, Madura JD, McCammon JA. Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme Biophysical Journal. 64: 9-15. PMID 8431552 DOI: 10.1016/S0006-3495(93)81335-3 |
0.645 |
|
| 1993 |
Luty BA, Wade RC, Madura JD, Davis ME, Briggs JM, McCammon JA. Brownian dynamics simulations of diffusional encounters between triose phosphate isomerase and glyceraldehyde phosphate: electrostatic steering of glyceraldehyde phosphate The Journal of Physical Chemistry. 97: 233-237. DOI: 10.1021/J100103A040 |
0.733 |
|
| 1992 |
Wade RC, McCammon JA. Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations. II. Calculation of free-energy differences by thermodynamic integration Journal of Molecular Biology. 225: 697-712. PMID 1318384 DOI: 10.1016/0022-2836(92)90395-Z |
0.422 |
|
| 1992 |
Wade RC, McCammon JA. Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations. I. Mapping the rotamers of residue 188 of viral protein 1 Journal of Molecular Biology. 225: 679-696. PMID 1318383 DOI: 10.1016/0022-2836(92)90394-Y |
0.482 |
|
| 1991 |
Wade RC, Mazor MH, McCammon JA, Quiocho FA. A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins Biopolymers. 31: 919-931. PMID 1782354 DOI: 10.1002/Bip.360310802 |
0.473 |
|
| 1990 |
Wade RC. Solvation of the active site of cytochrome P450-cam. Journal of Computer-Aided Molecular Design. 4: 199-204. PMID 2213064 DOI: 10.1007/Bf00125318 |
0.338 |
|
| 1990 |
Wade RC, Mazor MH, McCammon JA, Quiocho FA. Hydration of cavities in proteins: a molecular dynamics approach Journal of the American Chemical Society. 112: 7057-7059. DOI: 10.1021/Ja00175A048 |
0.488 |
|
| 1989 |
Reynolds CA, Wade RC, Goodford PJ. Identifying targets for bioreductive agents: Using GRID to predict selective binding regions of proteins Journal of Molecular Graphics. 7: 103-108. PMID 2488262 DOI: 10.1016/S0263-7855(89)80013-X |
0.365 |
|
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