Alexey Onufriev - Related publications

Virginia Polytechnic and State University, United States 
General Biophysics, Computer Science
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50 most relevant papers in past 60 days:
Year Citation  Score
2019 Roel-Touris J, Don CG, V Honorato R, Rodrigues JPGLM, Bonvin AMJJ. Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK. Journal of Chemical Theory and Computation. PMID 31539250 DOI: 10.1021/acs.jctc.9b00310   
2019 Galano-Frutos JJ, Sancho J. Accurate Calculation of Barnase and SNase Folding Energetics using short MD simulations and an Atomistic Model of the Unfolded Ensemble. Evaluation of Force Fields and Water Models. Journal of Chemical Information and Modeling. PMID 31513394 DOI: 10.1021/acs.jcim.9b00430   
2019 Shrestha UR, Juneja P, Zhang Q, Gurumoorthy V, Borreguero JM, Urban V, Cheng X, Pingali SV, Smith JC, O'Neill HM, Petridis L. Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation. Proceedings of the National Academy of Sciences of the United States of America. PMID 31548393 DOI: 10.1073/pnas.1907251116   
2019 Zheng L, Fan J, Mu Y. OnionNet: a Multiple-Layer Intermolecular-Contact-Based Convolutional Neural Network for Protein-Ligand Binding Affinity Prediction. Acs Omega. 4: 15956-15965. PMID 31592466 DOI: 10.1021/acsomega.9b01997   
2019 Lopez AJ, Pecora de Barros E, Martinez L. On the interpretation of subtilisin Carlsberg time-resolved fluorescence anisotropy decays: modeling with classical simulations. Journal of Chemical Information and Modeling. PMID 31524394 DOI: 10.1021/acs.jcim.9b00539   
2019 Pan Z, Wang Y, Gu X, Wang J, Cheng M. Refined Homology Model of Cytochrome Bcc Complex B Subunit for Virtual Screening of Potential Anti-Tuberculosis Agents. Journal of Biomolecular Structure & Dynamics. 1-17. PMID 31674290 DOI: 10.1080/07391102.2019.1688196   
2019 Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical Assessment of Methods of Protein Structure Prediction (CASP) - Round XIII. Proteins. PMID 31589781 DOI: 10.1002/prot.25823   
2019 Oliveira Junior AB, Yang H, Whitford PC, Leite VBP. Distinguishing biomolecular pathways and metastable states. Journal of Chemical Theory and Computation. PMID 31618581 DOI: 10.1021/acs.jctc.9b00704   
2019 Yang S, Liu H, Zhang Y, Lu H, Chen H. Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins. Journal of Chemical Information and Modeling. PMID 31613621 DOI: 10.1021/acs.jcim.9b00647   
2019 Allen AEA, Robertson MJ, Payne MC, Cole DJ. Development and Validation of the Quantum Mechanical Bespoke Protein Force Field. Acs Omega. 4: 14537-14550. PMID 31528808 DOI: 10.1021/acsomega.9b01769   
2019 McFarlane JMB, Krause K, Paci I. Accelerated Structural Prediction of Flexible Protein-Ligand Complexes: The SLICE Method. Journal of Chemical Information and Modeling. PMID 31693362 DOI: 10.1021/acs.jcim.9b00688   
2019 Wade AD, Huggins DJ. Optimization of Protein-Ligand Electrostatic Interactions Using an Alchemical Free-Energy Method. Journal of Chemical Theory and Computation. PMID 31584802 DOI: 10.1021/acs.jctc.9b00976   
2019 Kandathil SM, Garza-Fabre M, Handl J, Lovell SC. Reliable Generation of Native-Like Decoys Limits Predictive Ability in Fragment-Based Protein Structure Prediction. Biomolecules. 9. PMID 31618996 DOI: 10.3390/biom9100612   
2019 Doak DG, Denyer GS, Gerrard JA, Mackay JP, Allison JR. Peppy: A Virtual Reality Environment for Exploring the Principles of Polypeptide Structure. Protein Science : a Publication of the Protein Society. PMID 31622516 DOI: 10.1002/pro.3752   
2019 Corti R, Marrano CA, Salerno D, Brocca S, Natalello A, Santambrogio C, Legname G, Mantegazza F, Grandori R, Cassina V. Depicting Conformational Ensembles of α-Synuclein by Single Molecule Force Spectroscopy and Native Mass Spectroscopy. International Journal of Molecular Sciences. 20. PMID 31635031 DOI: 10.3390/ijms20205181   
2019 Lee JY, Krieger JM, Li H, Bahar I. Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations. Protein Science : a Publication of the Protein Society. PMID 31576621 DOI: 10.1002/pro.3732   
2019 Dos Santos RN, Bottino GF, Gozzo FC, Morcos F, Martínez L. Structural Complementarity of Distance Constraints Obtained from Chemical Crosslinking and Amino Acid Coevolution. Proteins. PMID 31693206 DOI: 10.1002/prot.25843   
2019 Akhter N, Chennupati G, Kabir KL, Djidjev H, Shehu A. Unsupervised and Supervised Learning over theEnergy Landscape for Protein Decoy Selection. Biomolecules. 9. PMID 31615116 DOI: 10.3390/biom9100607   
2019 Zheng W, Wuyun Q, Li Y, Mortuza SM, Zhang C, Pearce R, Ruan J, Zhang Y. Detecting distant-homology protein structures by aligning deep neural-network based contact maps. Plos Computational Biology. 15: e1007411. PMID 31622328 DOI: 10.1371/journal.pcbi.1007411   
2019 Gheibi N, Ghorbani M, Shariatifar H, Farasat A. In silico assessment of human Calprotectin subunits (S100A8/A9) in presence of sodium and calcium ions using Molecular Dynamics simulation approach. Plos One. 14: e0224095. PMID 31622441 DOI: 10.1371/journal.pone.0224095   
2019 Popov KI, Makepeace KAT, Petrotchenko EV, Dokholyan NV, Borchers CH. Insight into the Structure of the "Unstructured" Tau Protein. Structure (London, England : 1993). PMID 31628033 DOI: 10.1016/j.str.2019.09.003   
2019 Lemke T, Berg A, Jain A, Peter C. EncoderMap(II): Visualizing important molecular motions with improved generation of protein conformations. Journal of Chemical Information and Modeling. PMID 31647645 DOI: 10.1021/acs.jcim.9b00675   
2019 Huang SM, Yang F, Cai BY, He QT, Liu Q, Qu CX, Han MJ, Kong W, Jia YL, Li F, Yu X, Sun JP, Wang J. A Genetically Encoded Fluorescent Amino Acid for Monitoring Protein Interactions through FRET. Analytical Chemistry. PMID 31670502 DOI: 10.1021/acs.analchem.9b03305   
2019 Singh N, Villoutreix BO, Ecker GF. Rigorous sampling of docking poses unveils binding hypothesis for the halogenated ligands of L-type Amino acid Transporter 1 (LAT1). Scientific Reports. 9: 15061. PMID 31636293 DOI: 10.1038/s41598-019-51455-8   
2019 Lohia R, Salari R, Brannigan G. Sequence specificity despite intrinsic disorder: How a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein. Plos Computational Biology. 15: e1007390. PMID 31626641 DOI: 10.1371/journal.pcbi.1007390   
2019 Zhang HX, Xia QH, Zhou D. Effect of carbamylation on the molecular recognition action of amino benzothiazole by carrier protein. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 227: 117595. PMID 31675655 DOI: 10.1016/j.saa.2019.117595   
2019 Mondal M, Bhattacharyya D, Gao YQ. Structural properties and influence of solvent on the stability of telomeric four-stranded i-motif DNA. Physical Chemistry Chemical Physics : Pccp. PMID 31536074 DOI: 10.1039/c9cp03253c   
2019 Zhong S, Huang K, Xiao Z, Sheng X, Li Y, Duan L. Binding Mechanism of Thrombin-Ligand Systems Investigated by Polarized Protein-Specific Charge Force Field and Interaction Entropy Method. The Journal of Physical Chemistry. B. PMID 31532675 DOI: 10.1021/acs.jpcb.9b08064   
2019 Zhang D, Lazim R, Yip YM. Incorporating Polarizability of Backbone Hydrogen Bonds Improved Folding of Short α-Helical Peptides. Biophysical Journal. PMID 31685242 DOI: 10.1016/j.bpj.2019.10.020   
2019 Slavata L, Chmelík J, Kavan D, Filandrová R, Fiala J, Rosůlek M, Mrázek H, Kukačka Z, Vališ K, Man P, Miller M, McIntyre W, Fabris D, Novák P. MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex. Biomolecules. 9. PMID 31561554 DOI: 10.3390/biom9100535   
2019 Zou J, Simmerling C, Raleigh DP. Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid Experimental and Computational Approach. The Journal of Physical Chemistry. B. PMID 31702919 DOI: 10.1021/acs.jpcb.9b08323   
2019 Yan F, Liu X, Zhang S, Zhang Q, Chen J. Understanding Conformational Diversity of Heat Shock Protein 90 (HSP90) and Binding Features of Inhibitors to HSP90 via Molecular Dynamics Simulations. Chemical Biology & Drug Design. PMID 31560152 DOI: 10.1111/cbdd.13623   
2019 Mészáros B, Dobson L, Fichó E, Simon I. Sequence and Structure Properties Uncover the Natural Classification of Protein Complexes Formed by Intrinsically Disordered Proteins via Mutual Synergistic Folding. International Journal of Molecular Sciences. 20. PMID 31683980 DOI: 10.3390/ijms20215460   
2019 Li Z, Chen S, Gao C, Yang Z, Shih KC, Kochovski Z, Yang G, Gou L, Jiang M, Zhang L, Chen G. Chemically Controlled Helical Polymorphism in Protein Tubes by Selective Modulation of Supramolecular Interactions. Journal of the American Chemical Society. PMID 31710480 DOI: 10.1021/jacs.9b10505   
2019 Kamsri P, Punkvang A, Hannongbua S, Suttisintong K, Kittakoop P, Spencer J, Mulholland AJ, Pungpo P. In silico study directed towards identification of the key structural features of GyrB inhibitors targeting MTB DNA gyrase: HQSAR, CoMSIA and molecular dynamics simulations. Sar and Qsar in Environmental Research. 30: 775-800. PMID 31607177 DOI: 10.1080/1062936X.2019.1658218   
2019 Gao Y, Wang H, Wang J, Cheng M. In silico studies on p21-activated kinase 4 inhibitors: comprehensive application of 3D-QSAR analysis, molecular docking, molecular dynamics simulations and MM-GBSA calculation. Journal of Biomolecular Structure & Dynamics. 1-26. PMID 31556340 DOI: 10.1080/07391102.2019.1673823   
2019 Mazzier D, De S, Wicher B, Maurizot V, Huc I. Interplay of secondary and tertiary folding in abiotic foldamers. Chemical Science. 10: 6984-6991. PMID 31588265 DOI: 10.1039/c9sc01322a   
2019 Potthoff J, Bojarski KK, Kohut G, Lipska AG, Liwo A, Kessler E, Ricard-Blum S, Samsonov SA. Analysis of Procollagen C-Proteinase Enhancer-1/Glycosaminoglycan Binding Sites and of the Potential Role of Calcium Ions in the Interaction. International Journal of Molecular Sciences. 20. PMID 31658765 DOI: 10.3390/ijms20205021   
2019 Srivastava D, Artemyev NO. Large-scale conformational rearrangement of the α5-helix of Gα subunits in complex with the guanine nucleotide exchange factor Ric8A. The Journal of Biological Chemistry. PMID 31624147 DOI: 10.1074/jbc.AC119.011135   
2019 He Q, Chu H, Wang Y, Guo H, Wang Y, Wang S, Feng Z, Xie XQ, Hu Y, Liu H, Lin Z. In silico design novel Vibsanin B derivatives as inhibitor for heat shock protein 90 based on 3D-QSAR, molecular docking and molecular dynamics simulation. Journal of Biomolecular Structure & Dynamics. 1-13. PMID 31542999 DOI: 10.1080/07391102.2019.1671900   
2019 Srivastava S, Mehta P, Sharma O, Sharma M, Malik R. Computationally guided identification of Akt-3, a serine/threonine kinase inhibitors: Insights from homology modelling, structure-based screening, molecular dynamics and quantum mechanical calculations. Journal of Biomolecular Structure & Dynamics. 1-11. PMID 31590614 DOI: 10.1080/07391102.2019.1675536   
2019 Guseynov AD, Pisarev SA, Shulga DA, Palyulin VA, Fedorov MV, Karlov DS. Computational characterization of the glutamate receptor antagonist perampanel and its close analogs: density functional exploration of conformational space and molecular docking study. Journal of Molecular Modeling. 25: 312. PMID 31511986 DOI: 10.1007/s00894-019-4188-z   
2019 Tyrikos-Ergas T, Fittolani G, Seeberger PH, Delbianco M. Structural studies using unnatural oligosaccharides: towards sugar foldamers. Biomacromolecules. PMID 31517479 DOI: 10.1021/acs.biomac.9b01090   
2019 Ravasio R, Flatt SM, Yan L, Zamuner S, Brito C, Wyart M. Mechanics of Allostery: Contrasting the Induced Fit and Population Shift Scenarios. Biophysical Journal. PMID 31653447 DOI: 10.1016/j.bpj.2019.10.002   
2019 Mura C, Veretnik S, Bourne PE. The Urfold: Structural Similarity Just above the Superfold Level? Protein Science : a Publication of the Protein Society. PMID 31599042 DOI: 10.1002/pro.3742   
2019 Sakae Y, Zhang BW, Levy RM, Deng N. Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses. Journal of Computational Chemistry. PMID 31621932 DOI: 10.1002/jcc.26078   
2019 Wakamoto T, Ikeya T, Kitazawa S, Baxter NJ, Williamson MP, Kitahara R. Paramagnetic relaxation enhancement-assisted structural characterization of a partially disordered conformation of ubiquitin. Protein Science : a Publication of the Protein Society. PMID 31587403 DOI: 10.1002/pro.3734   
2019 Sood D, Kumar N, Singh A, Tomar V, Dass SK, Chandra R. Deciphering the Binding Mechanism of Noscapine with Lysozyme: Biophysical and Chemoinformatic Approaches. Acs Omega. 4: 16233-16241. PMID 31592173 DOI: 10.1021/acsomega.9b02578   
2019 Guterres H, Lee HS, Im W. Ligand-Binding Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates. Journal of Chemical Theory and Computation. PMID 31557013 DOI: 10.1021/acs.jctc.9b00751   
2019 Wang R, Xu D. Molecular dynamics investigations of oligosaccharides recognized by family 16 and 22 carbohydrate binding modules. Physical Chemistry Chemical Physics : Pccp. PMID 31535114 DOI: 10.1039/c9cp04673a