Julio Omar Ortiz, Dr. - Related publications

Max Planck Institute of Biochemistry Martinsried / Munich 
Cryo-electron Tomography, Cell biology, Translation, Ribosomes
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Vankayala SL, Warrensford LC, Pittman AR, Pollard BC, Kearns FL, Larkin JD, Woodcock HL. CIFDock: A novel CHARMM-based flexible receptor-flexible ligand docking protocol. Journal of Computational Chemistry. PMID 34741467 DOI: 10.1002/jcc.26759   
2021 Zhao Q, Yuan JJ, Hu F, Qian C, Tian CF, Wang JT, Gao D, Yi W, Wang HB. Isolation, physicochemical, and structure-function relationship of the hydrophobic variant of Fc-fusion proteins that bind to TNF-α receptor, HS002 and HS002A. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 1186: 123026. PMID 34781108 DOI: 10.1016/j.jchromb.2021.123026   
2021 Tanramluk D*, Pakotiprapha D, Phoochaijaroen S, Chantravisut P, Thampradid S, Vanichtanankul J, Narupiyakul L, Akavipat R, Yuvaniyama J. MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances. Structure. PMID 34614393 DOI: 10.1016/j.str.2021.09.004   
2021 He T, Liu J, Wang JP. Development of a Dihydropteroate Synthase-Based Fluorescence Polarization Assay for Detection of Sulfonamides and Studying Its Recognition Mechanism. Journal of Agricultural and Food Chemistry. PMID 34783550 DOI: 10.1021/acs.jafc.1c05674   
2021 Jiang Z, Xiao SR, Liu R. Dissecting and predicting different types of binding sites in nucleic acids based on structural information. Briefings in Bioinformatics. PMID 34624074 DOI: 10.1093/bib/bbab411   
2021 Heltberg ML, Miné-Hattab J, Taddei A, Walczak AM, Mora T. Physical observables to determine the nature of membrane-less cellular sub-compartments. Elife. 10. PMID 34677123 DOI: 10.7554/eLife.69181   
2021 Sun Z, Zheng S, Zhao H, Niu Z, Lu Y, Pan Y, Yang Y. To improve the predictions of binding residues with DNA, RNA, carbohydrate, and peptide via multi-task deep neural networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34637380 DOI: 10.1109/TCBB.2021.3118916   
2021 Schwarz M, Eno RFM, Freitag-Pohl S, Coxon CR, Straker HE, Wortley DJ, Hughes DJ, Mitchell G, Moore J, Cummins I, Onkokesung N, Brazier-Hicks M, Edwards R, Pohl E, Steel PG. Flavonoid-based inhibitors of the Phi-class glutathione transferase from black-grass to combat multiple herbicide resistance. Organic & Biomolecular Chemistry. PMID 34643629 DOI: 10.1039/d1ob01802g   
2021 Cuy-Chaparro L, Bohórquez MD, Arévalo-Pinzón G, Castañeda-Ramírez JJ, Suárez CF, Pabón L, Ordóñez D, Gallego-López GM, Suárez CE, Moreno-Pérez DA, Patarroyo MA. Ligand-Receptor Interaction: AMA-1 Contains Small Regions Governing Bovine Erythrocyte Binding. International Journal of Molecular Sciences. 22. PMID 33450807 DOI: 10.3390/ijms22020714   
2021 Correia VG, Trovão F, Pinheiro BA, Brás JLA, Silva LM, Nunes C, Coimbra MA, Liu Y, Feizi T, Fontes CMGA, Mulloy B, Chai W, Carvalho AL, Palma AS. Mapping Molecular Recognition of β1,3-1,4-Glucans by a Surface Glycan-Binding Protein from the Human Gut Symbiont Bacteroides ovatus. Microbiology Spectrum. e0182621. PMID 34817219 DOI: 10.1128/Spectrum.01826-21   
2021 Robertson AJ, Courtney JM, Shen Y, Ying J, Bax A. Concordance of X-ray and AlphaFold2 Models of SARS-CoV-2 Main Protease with Residual Dipolar Couplings Measured in Solution. Journal of the American Chemical Society. PMID 34757725 DOI: 10.1021/jacs.1c10588   
2021 Xu L, Zhao L, Che J, Zhang Q, Cao R, Li X. Identification of novel influenza polymerase PB2 inhibitors using virtual screening approach and molecular dynamics simulation analysis of active compounds. Bioorganic & Medicinal Chemistry. 52: 116515. PMID 34839161 DOI: 10.1016/j.bmc.2021.116515   
2021 Keshtvarz M, Mahboobi M, Kieliszek M, Miecznikowski A, Sedighian H, Rezaei M, Haghighi MA, Zareh Z, Rezaei E. Engineering of Cytolethal Distending Toxin B by Its Reducing Immunogenicity and Maintaining Stability as a New Drug Candidate for Tumor Therapy; an In Silico Study. Toxins. 13. PMID 34822569 DOI: 10.3390/toxins13110785   
2021 Berta D, Badaoui M, Martino SA, Buigues PJ, Pisliakov AV, Elghobashi-Meinhardt N, Wells G, Harris SA, Frezza E, Rosta E. Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design. Chemical Science. 12: 13492-13505. PMID 34777769 DOI: 10.1039/d1sc02775a   
2021 Dang M, Song J. CTD of SARS-CoV-2 N protein is a cryptic domain for binding ATP and nucleic acid that interplay in modulating phase separation. Protein Science : a Publication of the Protein Society. PMID 34734665 DOI: 10.1002/pro.4221   
2021 Essegian DJ, Cunningham TA, Zerio CJ, Chapman E, Schatz J, Schürer SC. Molecular Dynamics Simulations Identify Tractable Lead-like Phenyl-Piperazine Scaffolds as eIF4A1 ATP-competitive Inhibitors. Acs Omega. 6: 24432-24443. PMID 34604625 DOI: 10.1021/acsomega.1c02805   
2021 Zhu L, Jiang H, Cao S, Unarta IC, Gao X, Huang X. Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex. Communications Biology. 4: 1345. PMID 34848812 DOI: 10.1038/s42003-021-02822-7   
2021 Islam MA, Rallabandi VPS, Mohammed S, Srinivasan S, Natarajan S, Dudekula DB, Park J. Screening of β1- and β2-Adrenergic Receptor Modulators through Advanced Pharmacoinformatics and Machine Learning Approaches. International Journal of Molecular Sciences. 22. PMID 34681845 DOI: 10.3390/ijms222011191   
2021 Yin V, Lai SH, Caniels TG, Brouwer PJM, Brinkkemper M, Aldon Y, Liu H, Yuan M, Wilson IA, Sanders RW, van Gils MJ, Heck AJR. Probing Affinity, Avidity, Anticooperativity, and Competition in Antibody and Receptor Binding to the SARS-CoV-2 Spike by Single Particle Mass Analyses. Acs Central Science. 7: 1863-1873. PMID 34845440 DOI: 10.1021/acscentsci.1c00804   
2021 Sapienza PJ, Currie MM, Lancaster NM, Li K, Aubé J, Goldfarb D, Cloer EW, Major MB, Lee AL. Visualizing an Allosteric Intermediate Using CuAAC Stabilization of an NMR Mixed Labeled Dimer. Acs Chemical Biology. PMID 34784173 DOI: 10.1021/acschembio.1c00617   
2021 Zackria AA, Pattabiraman R, Murthy TPK, Kumar SB, Mathew BB, Biju VG. Computational screening of natural compounds from R. Br. for inhibition of SARS-CoV-2 main protease. Vegetos (Bareilly, India). 1-15. PMID 34690453 DOI: 10.1007/s42535-021-00304-z   
2021 Zagotta WN, Sim BS, Nhim AK, Raza MM, Evans EG, Venkatesh Y, Jones CM, Mehl RA, Petersson EJ, Gordon SE. An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET. Elife. 10. PMID 34623258 DOI: 10.7554/eLife.70236   
2021 Kolos JM, Pomplun S, Jung S, Rieß B, Purder PL, Voll AM, Merz S, Gnatzy M, Geiger TM, Quist-Løkken I, Jatzlau J, Knaus P, Holien T, Bracher A, Meyners C, et al. Picomolar FKBP inhibitors enabled by a single water-displacing methyl group in bicyclic [4.3.1] aza-amides. Chemical Science. 12: 14758-14765. PMID 34820091 DOI: 10.1039/d1sc04638a   
2021 Meng D, Zhang L, Wang Q, Zhang Y, Sun Y, Zhang H, Wang Z, Zhou Z, Yang R. Self-Assembly of Phycoerythrin with Oligochitosan by Electrostatic Interaction for Stabilization of Phycoerythrin. Journal of Agricultural and Food Chemistry. PMID 34669400 DOI: 10.1021/acs.jafc.1c05205   
2021 Dickerhoff J, Brundridge N, McLuckey SA, Yang D. Berberine Molecular Recognition of the Parallel MYC G-Quadruplex in Solution. Journal of Medicinal Chemistry. 64: 16205-16212. PMID 34677968 DOI: 10.1021/acs.jmedchem.1c01508   
2021 Adegawa S, Yamaguchi N, Sato R. The base and root of domain II loops of Cry toxins contribute to binding to Bombyx mori ABC transporter C2. The Febs Journal. PMID 34618400 DOI: 10.1111/febs.16224   
2021 Vongsouthi V, Whitfield JH, Unichenko P, Mitchell JA, Breithausen B, Khersonsky O, Kremers L, Janovjak H, Monai H, Hirase H, Fleishman SJ, Henneberger C, Jackson CJ. A Rationally and Computationally Designed Fluorescent Biosensor for d-Serine. Acs Sensors. 6: 4193-4205. PMID 34783546 DOI: 10.1021/acssensors.1c01803   
2021 Ali A, Abdellattif MH, Ali A, AbuAli O, Shahbaaz M, Ahsan MJ, Hussien MA. Computational Approaches for the Design of Novel Anticancer Compounds Based on Pyrazolo[3,4-d]pyrimidine Derivatives as TRAP1 Inhibitor. Molecules (Basel, Switzerland). 26. PMID 34641473 DOI: 10.3390/molecules26195932   
2021 Ashraf S, Ranaghan KE, Woods CJ, Mulholland AJ, Ul-Haq Z. Exploration of the structural requirements of Aurora Kinase B inhibitors by a combined QSAR, modelling and molecular simulation approach. Scientific Reports. 11: 18707. PMID 34548506 DOI: 10.1038/s41598-021-97368-3   
2021 Plessa E, Chu LP, Chan SHS, Thomas OL, Cassaignau AME, Waudby CA, Christodoulou J, Cabrita LD. Nascent chains can form co-translational folding intermediates that promote post-translational folding outcomes in a disease-causing protein. Nature Communications. 12: 6447. PMID 34750347 DOI: 10.1038/s41467-021-26531-1   
2021 Rübbelke M, Hamilton J, Binder F, Bauer M, King J, Nar H, Zeeb M. Discovery and Structure-Based Optimization of Fragments Binding the Mixed Lineage Kinase Domain-like Protein Executioner Domain. Journal of Medicinal Chemistry. PMID 34672548 DOI: 10.1021/acs.jmedchem.1c00686   
2021 Lamichhane TR, Ghimire MP. Evaluation of SARS-CoV-2 main protease and inhibitor interactions using dihedral angle distributions and radial distribution function. Heliyon. 7: e08220. PMID 34693066 DOI: 10.1016/j.heliyon.2021.e08220   
2021 Seok J, Hong J, Park J, Kim KJ. Structural analysis of the peptidoglycan editing factor PdeF from Bacillus cereus ATCC 14579. Biochemical and Biophysical Research Communications. 583: 43-48. PMID 34735878 DOI: 10.1016/j.bbrc.2021.10.051   
2021 Clyde A, Galanie S, Kneller DW, Ma H, Babuji Y, Blaiszik B, Brace A, Brettin T, Chard K, Chard R, Coates L, Foster I, Hauner D, Kertesz V, Kumar N, et al. High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. Journal of Chemical Information and Modeling. PMID 34793155 DOI: 10.1021/acs.jcim.1c00851   
2021 Heyne M, Shirian J, Cohen I, Peleg Y, Radisky ES, Papo N, Shifman JM. Climbing Up and Down Binding Landscapes through Deep Mutational Scanning of Three Homologous Protein-Protein Complexes. Journal of the American Chemical Society. PMID 34609866 DOI: 10.1021/jacs.1c08707   
2021 Hendrikse SIS, Contreras-Montoya R, Ellis AV, Thordarson P, Steed JW. Biofunctionality with a twist: the importance of molecular organisation, handedness and configuration in synthetic biomaterial design. Chemical Society Reviews. PMID 34846055 DOI: 10.1039/d1cs00896j   
2021 Kumar BH, Manandhar S, Mehta CH, Nayak UY, Pai KSR. Structure-based docking, pharmacokinetic evaluation, and molecular dynamics-guided evaluation of traditional formulation against SARS-CoV-2 spike protein receptor bind domain and ACE2 receptor complex. Chemicke Zvesti. 1-21. PMID 34690412 DOI: 10.1007/s11696-021-01917-z   
2021 Numoto N, Kawano Y, Okumura H, Baba S, Fukumori Y, Miki K, Ito N. Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state. Iucrj. 8: 954-962. PMID 34804547 DOI: 10.1107/S2052252521009386   
2021 Kou SB, Li L, Zhang RJ, Shi JH, Jiang SL. Elucidation of the interaction mechanism of olmutinib with human α-1 acid glycoprotein: insights from spectroscopic and molecular modeling studies. Journal of Biomolecular Structure & Dynamics. 1-13. PMID 34844510 DOI: 10.1080/07391102.2021.2009373   
2021 Gisriel CJ, Flesher DA, Shen G, Wang J, Ho MY, Brudvig GW, Bryant DA. Structure of a photosystem I-ferredoxin complex from a marine cyanobacterium provides insights into far-red light photoacclimation. The Journal of Biological Chemistry. 101408. PMID 34793839 DOI: 10.1016/j.jbc.2021.101408   
2021 Zong K, Xu L, Hou Y, Zhang Q, Che J, Zhao L, Li X. Virtual Screening and Molecular Dynamics Simulation Study of Influenza Polymerase PB2 Inhibitors. Molecules (Basel, Switzerland). 26. PMID 34834044 DOI: 10.3390/molecules26226944   
2021 Baucom DR, Furr M, Kumar VG, Okoto P, Losey JL, Henry RL, Moradi M, Suresh Kumar TK, Heyes CD. Transient Local Secondary Structure in the Intrinsically Disordered C-Term of the Albino3 Insertase. Biophysical Journal. PMID 34662559 DOI: 10.1016/j.bpj.2021.10.013   
2021 Raj N, Click T, Yang H, Chu JW. Mechanical couplings of protein backbone and side chains exhibit scale-free network properties and specific hotspots for function. Computational and Structural Biotechnology Journal. 19: 5309-5320. PMID 34765086 DOI: 10.1016/j.csbj.2021.09.004   
2021 Catalano C, Al Mughram MH, Guo Y, Kellogg GE. 3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins. Current Research in Structural Biology. 3: 239-256. PMID 34693344 DOI: 10.1016/j.crstbi.2021.09.002   
2021 Wong SWK, Liu Z. Conformational variability of loops in the SARS-CoV-2 spike protein. Proteins. PMID 34661307 DOI: 10.1002/prot.26266   
2021 Purushothaman M, Dhar SK, Natesh R. Role of unique loops in oligomerization and ATPase function of Plasmodium falciparum gyrase B. Protein Science : a Publication of the Protein Society. PMID 34716632 DOI: 10.1002/pro.4217   
2021 Wang Z, Zheng L, Liu Y, Qu Y, Li YQ, Zhao M, Mu Y, Li W. OnionNet-2: A Convolutional Neural Network Model for Predicting Protein-Ligand Binding Affinity Based on Residue-Atom Contacting Shells. Frontiers in Chemistry. 9: 753002. PMID 34778208 DOI: 10.3389/fchem.2021.753002   
2021 Yan M, Dong S, Shen X, Lu C, Ye H, Zhang T. Lactoferrin-thymol complex for the disinfection of gram-positive and Gram-negative . Food & Function. PMID 34633016 DOI: 10.1039/d1fo02153b   
2021 Gaurav M, Natesh A, Arundhati A, Mariam D. Biochemical aspects of hemoglobin-xenobiotic interactions and their implications in drug discovery. Biochimie. 191: 154-163. PMID 34474139 DOI: 10.1016/j.biochi.2021.08.006   
2021 Peng CY, Zhu HD, Zhang L, Li XF, Zhou WN, Tu ZC. Urolithin A alleviates advanced glycation end-product formation by altering protein structures, trapping methylglyoxal and forming complexes. Food & Function. PMID 34734623 DOI: 10.1039/d1fo02631c