Alexey Onufriev - Related publications

Affiliations: 
Virginia Polytechnic and State University, United States 
Area:
General Biophysics, Computer Science
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Deflorian F, Perez-Benito L, Lenselink EB, Congreve M, van Vlijmen HWT, Mason JS, Graaf C, Tresadern G. Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation. Journal of Chemical Information and Modeling. PMID 32539374 DOI: 10.1021/acs.jcim.0c00449   
2020 Tao P, Xiao Y. Using the generalized Born surface area model to fold proteins yields more effective sampling while qualitatively preserving the folding landscape. Physical Review. E. 101: 062417. PMID 32688556 DOI: 10.1103/PhysRevE.101.062417   
2020 Michael E, Polydorides S, Simonson T, Archontis G. Hybrid MC/MD for protein design. The Journal of Chemical Physics. 153: 054113. PMID 32770896 DOI: 10.1063/5.0013320   
2020 Oliveira NFB, Pires IDS, Machuqueiro M. Improved GROMOS 54A7 charge sets for phosphorylated Tyr, Ser, and Thr to deal with pH-dependent binding phenomena. Journal of Chemical Theory and Computation. PMID 32809819 DOI: 10.1021/acs.jctc.0c00529   
2020 Tan YS, Verma CS. Straightforward incorporation of multiple ligand types into molecular dynamics simulations for efficient binding site detection and characterization. Journal of Chemical Theory and Computation. PMID 32810406 DOI: 10.1021/acs.jctc.0c00405   
2020 Smith Z, Ravindra P, Wang Y, Cooley R, Tiwary P. Discovering Protein Conformational Flexibility Through Artificial Intelligence Aided Molecular Dynamics. The Journal of Physical Chemistry. B. PMID 32841026 DOI: 10.1021/acs.jpcb.0c03985   
2020 Ozgur B, Sayar M. Representation of the conformational ensemble of peptides in coarse grained simulations. The Journal of Chemical Physics. 153: 054108. PMID 32770883 DOI: 10.1063/5.0012391   
2020 Suating P, Nguyen TT, Ernst NE, Wang Y, Jordan JH, Gibb CLD, Ashbaugh HS, Gibb BC. Proximal charge effects on guest binding to a non-polar pocket. Chemical Science. 11: 3656-3663. PMID 32864079 DOI: 10.1039/c9sc06268h   
2020 Chen M, Chen X, Jin S, Lu W, Lin X, Wolynes PG. Protein Structure Refinement Guided by Atomic Packing Frustration Analysis. The Journal of Physical Chemistry. B. PMID 32931278 DOI: 10.1021/acs.jpcb.0c06719   
2020 Chen M, Chen X, Jin S, Lu W, Lin X, Wolynes PG. Protein Structure Refinement Guided by Atomic Packing Frustration Analysis. The Journal of Physical Chemistry. B. PMID 32931278 DOI: 10.1021/acs.jpcb.0c06719   
2020 Schneider J, Korshunova K, Si Chaib Z, Giorgetti A, Alfonso-Prieto M, Carloni P. Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-Based Hybrid Molecular Mechanics/Coarse-Grained Approach. Journal of Chemical Information and Modeling. PMID 32786708 DOI: 10.1021/acs.jcim.0c00661   
2020 Dasari S, Mallik BS. Conformational Free Energy Landscapes of Alanine Dipeptide in Hydrated Ionic Liquids from Enhanced Sampling Methods. The Journal of Physical Chemistry. B. PMID 32666802 DOI: 10.1021/acs.jpcb.0c05629   
2020 Macchiagodena M, Pagliai M, Andreini C, Rosato A, Procacci P. Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins. Acs Omega. 5: 15301-15310. PMID 32637803 DOI: 10.1021/acsomega.0c01337   
2020 Liu K, Kokubo H. Prediction of ligand binding mode among multiple cross-docking poses by molecular dynamics simulations. Journal of Computer-Aided Molecular Design. PMID 32869148 DOI: 10.1007/s10822-020-00340-y   
2020 Herrera-Nieto P, Pérez A, De Fabritiis G. Small molecule modulation of intrinsically disordered proteins using molecular dynamics simulations. Journal of Chemical Information and Modeling. PMID 32786705 DOI: 10.1021/acs.jcim.0c00381   
2020 Zhang Y, Cao Z, Zhang JZH, Xia F. A Double-Well Ultra-Coarse-Grained Model to Describe Protein Conformational Transitions. Journal of Chemical Theory and Computation. PMID 32926616 DOI: 10.1021/acs.jctc.0c00551   
2020 Bian Y, Song F, Zhang J, Yu J, Wang J, Wang W. Insights into the kinetic partitioning folding dynamics of human telomeric G-quadruplex from molecular simulations and machine learning. Journal of Chemical Theory and Computation. PMID 32794754 DOI: 10.1021/acs.jctc.0c00340   
2020 Jawad B, Poudel L, Podgornik R, Ching WY. Thermodynamic dissection of the intercalation binding process of doxorubicin to dsDNA with implications of ionic and solvent effects. The Journal of Physical Chemistry. B. PMID 32786213 DOI: 10.1021/acs.jpcb.0c05840   
2020 Lincoff J, Haghighatlari M, Krzeminski M, Teixeira JMC, Gomes GW, Gradinaru CC, Forman-Kay JD, Head-Gordon T. Extended Experimental Inferential Structure Determination Method in Determining the Structural Ensembles of Disordered Protein States. Communications Chemistry. 3. PMID 32775701 DOI: 10.1038/s42004-020-0323-0   
2020 Neelamraju S, Wales DJ, Gosavi S. Protein energy landscape exploration with structure-based models. Current Opinion in Structural Biology. 64: 145-151. PMID 32795948 DOI: 10.1016/j.sbi.2020.07.003   
2020 Polyakov IV, Kniga AE, Grigorenko BL, Nemukhin AV. Structure of the Brain -Acetylaspartate Biosynthetic Enzyme NAT8L Revealed by Computer Modeling. Acs Chemical Neuroscience. 11: 2296-2302. PMID 32639720 DOI: 10.1021/acschemneuro.0c00250   
2020 Amera GM, Khan RJ, Pathak A, Jha RK, Jain M, Muthukumaran J, Singh AK. Structure based drug designing and discovery of promising lead molecules against UDP-N-acetylenolpyruvoylglucosamine reductase (MurB): A potential drug target in multi-drug resistant Acinetobacter baumannii. Journal of Molecular Graphics & Modelling. 100: 107675. PMID 32731183 DOI: 10.1016/j.jmgm.2020.107675   
2020 Kadukova M, Machado KDS, Chacón P, Grudinin S. KORP-PL: a coarse-grained knowledge-based scoring function for protein-ligand interactions. Bioinformatics (Oxford, England). PMID 32840574 DOI: 10.1093/bioinformatics/btaa748   
2020 Bergonzo C, Szakal AL. Using All-Atom Potentials to Refine RNA Structure Predictions of SARS-CoV-2 Stem Loops. International Journal of Molecular Sciences. 21. PMID 32867123 DOI: 10.3390/ijms21176188   
2020 Grant BJ, Skjaerven L, Yao XQ. The Bio3D Packages for Structural Bioinformatics. Protein Science : a Publication of the Protein Society. PMID 32734663 DOI: 10.1002/pro.3923   
2020 Ahmad F, Shabaz Z, Azam SS. Insight into natural inhibitors and bridging docking to dynamic simulation against sugar Isomerase (SIS) domain protein. Journal of Molecular Modeling. 26: 221. PMID 32748070 DOI: 10.1007/s00894-020-04475-5   
2020 Rahman MM, Saha T, Islam KJ, Suman RH, Biswas S, Rahat EU, Hossen MR, Islam R, Hossain MN, Mamun AA, Khan M, Ali MA, Halim MA. Virtual screening, molecular dynamics and structure-activity relationship studies to identify potent approved drugs for Covid-19 treatment. Journal of Biomolecular Structure & Dynamics. 1-11. PMID 32692306 DOI: 10.1080/07391102.2020.1794974   
2020 Rackovsky S, Scheraga HA. The structure of protein dynamic space. Proceedings of the National Academy of Sciences of the United States of America. PMID 32759212 DOI: 10.1073/pnas.2008873117   
2020 Gur M, Taka E, Yilmaz SZ, Kilinc C, Aktas U, Golcuk M. Conformational transition of SARS-CoV-2 spike glycoprotein between its closed and open states. The Journal of Chemical Physics. 153: 075101. PMID 32828084 DOI: 10.1063/5.0011141   
2020 Silva SVRL, Silva PJ. Computational improvement of small-molecule inhibitors of protective antigen activation through isostere-based substitutions. Journal of Biomolecular Structure & Dynamics. 1-9. PMID 32662753 DOI: 10.1080/07391102.2020.1792987   
2020 Choi Y, Jeong S, Choi JM, Ndong C, Griswold KE, Bailey-Kellogg C, Kim HS. Computer-guided binding mode identification and affinity improvement of an LRR protein binder without structure determination. Plos Computational Biology. 16: e1008150. PMID 32866140 DOI: 10.1371/journal.pcbi.1008150   
2020 Liu C, Brini E, Perez A, Dill KA. Computing ligands bound to proteins using MELD-accelerated MD. Journal of Chemical Theory and Computation. PMID 32910647 DOI: 10.1021/acs.jctc.0c00543   
2020 Conrad M, Söldner CA, Miao Y, Sticht H. Agonist Binding and G Protein Coupling in Histamine H Receptor: A Molecular Dynamics Study. International Journal of Molecular Sciences. 21. PMID 32932742 DOI: 10.3390/ijms21186693   
2020 Bertuzzi S, Gimeno A, Nuñez R, Bernardo-Seisdedos G, Delgado S, Jimenez-Oses G, Millet O, Jimenez-Barbero J, Arda A. Unravelling the time scale of conformational plasticity and allostery in glycan recognition by human galectin-1. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 32780906 DOI: 10.1002/chem.202003212   
2020 Li X, Liu H, Gao C, Li Y, Jia D, Yang Y, Yang J, Wei Z, Jiang T, Yu R. ConoMode, a database for conopeptide binding modes. Database : the Journal of Biological Databases and Curation. 2020. PMID 32754758 DOI: 10.1093/database/baaa058   
2020 Li X, Liu H, Gao C, Li Y, Jia D, Yang Y, Yang J, Wei Z, Jiang T, Yu R. ConoMode, a database for conopeptide binding modes. Database : the Journal of Biological Databases and Curation. 2020. PMID 32754758 DOI: 10.1093/database/baaa058   
2020 Lokhande KB, Doiphode S, Vyas R, Swamy KV. Molecular docking and simulation studies on SARS-CoV-2 M reveals Mitoxantrone, Leucovorin, Birinapant, and Dynasore as potent drugs against COVID-19. Journal of Biomolecular Structure & Dynamics. 1-12. PMID 32815481 DOI: 10.1080/07391102.2020.1805019   
2020 Miller MC, Nesmelova IV, Daragan VA, Ippel H, Michalak M, Dregni A, Kaltner H, Kopitz J, Gabius HJ, Mayo KH. Pro4 prolyl peptide bond isomerization in human galectin-7 modulates the monomer-dimer equilibrum to affect function. The Biochemical Journal. PMID 32766716 DOI: 10.1042/BCJ20200499   
2020 Taguchi AT, Boyd J, Diehnelt CW, Legutki JB, Zhao ZG, Woodbury NW. Comprehensive Prediction of Molecular Recognition in a Combinatorial Chemical Space Using Machine Learning. Acs Combinatorial Science. PMID 32786325 DOI: 10.1021/acscombsci.0c00003   
2020 Kirmizialtin S, Pitici F, Cardenas AE, Elber R, Thirumalai D. Dramatic Shape Changes Occur as Cytochrome Folds. The Journal of Physical Chemistry. B. PMID 32840372 DOI: 10.1021/acs.jpcb.0c05802   
2020 Ma H, Zou T, Li H, Cheng H. The interaction of sodium dodecyl sulfate with trypsin: Multi-spectroscopic analysis, molecular docking, and molecular dynamics simulation. International Journal of Biological Macromolecules. PMID 32781131 DOI: 10.1016/j.ijbiomac.2020.08.020   
2020 Ma H, Zou T, Li H, Cheng H. The interaction of sodium dodecyl sulfate with trypsin: Multi-spectroscopic analysis, molecular docking, and molecular dynamics simulation. International Journal of Biological Macromolecules. PMID 32781131 DOI: 10.1016/j.ijbiomac.2020.08.020   
2020 Kramer CAC, da Silva ARL, de Carvalho LS. Influence of phenylpropanoid units of lignin and its oxidized derivatives on the stability and βO4 binding properties: DFT and QTAIM approach. Organic & Biomolecular Chemistry. PMID 32685944 DOI: 10.1039/d0ob01171a   
2020 Baildya N, Ghosh NN, Chattopadhyay AP. Inhibitory activity of hydroxychloroquine on COVID-19 main protease: An insight from MD-simulation studies. Journal of Molecular Structure. 1219: 128595. PMID 32834108 DOI: 10.1016/j.molstruc.2020.128595   
2020 Tambe PM, Bhowmick S, Chaudhary SK, Khan MR, Wabaidur SM, Muddassir M, Patil PC, Islam MA. Structure-Based Screening of DNA GyraseB Inhibitors for Therapeutic Applications in Tuberculosis: a Pharmacoinformatics Study. Applied Biochemistry and Biotechnology. PMID 32686004 DOI: 10.1007/s12010-020-03374-y   
2020 Senior T, Botha MJ, Kennedy AR, Calvo-Castro J. Understanding the Contribution of Individual Amino Acid Residues in the Binding of Psychoactive Substances to Monoamine Transporters. Acs Omega. 5: 17223-17231. PMID 32715208 DOI: 10.1021/acsomega.0c01370   
2020 Dai Y, Li Y, Wang L, Peng Z, Yang J. On monomeric and multimeric structures-based protein-ligand interactions. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 32750865 DOI: 10.1109/TCBB.2020.3002776   
2020 Chen PC, Masiewicz P, Perez K, Hennig J. Structure-based screening of binding affinities via small-angle X-ray scattering. Iucrj. 7: 644-655. PMID 32695411 DOI: 10.1107/S2052252520004169   
2020 Dos Santos EG, Faria RX, Rodrigues CR, Bello ML. Molecular dynamic simulations of full-length human purinergic receptor subtype P2X7 bonded to potent inhibitors. European Journal of Pharmaceutical Sciences : Official Journal of the European Federation For Pharmaceutical Sciences. 152: 105454. PMID 32629018 DOI: 10.1016/j.ejps.2020.105454   
2020 Horx P, Geyer A. Defining the mobility range of a hinge-type connection using molecular dynamics and metadynamics. Plos One. 15: e0230962. PMID 32282813 DOI: 10.1371/journal.pone.0230962