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Alexey Onufriev - Publications

Affiliations: 
Virginia Polytechnic Institute and State University, Blacksburg, VA, United States 
Area:
General Biophysics, Computer Science
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37 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2025 Amaro RE, Åqvist J, Bahar I, Battistini F, Bellaiche A, Beltran D, Biggin PC, Bonomi M, Bowman GR, Bryce RA, Bussi G, Carloni P, Case DA, Cavalli A, Chang CA, ... ... Onufriev A, et al. The need to implement FAIR principles in biomolecular simulations. Nature Methods. PMID 40175561 DOI: 10.1038/s41592-025-02635-0  0.466
2023 Onufriev AV. Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome. Frontiers in Molecular Biosciences. 10: 1067787. PMID 37143824 DOI: 10.3389/fmolb.2023.1067787  0.311
2020 Forouzesh N, Onufriev AV. MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor. Biorxiv : the Preprint Server For Biology. PMID 32869029 DOI: 10.1101/2020.08.25.267625  0.317
2019 Shabane PS, Izadi S, Onufriev AV. A general purpose water model can improve atomistic simulations of intrinsically disordered proteins. Journal of Chemical Theory and Computation. PMID 30865832 DOI: 10.1021/acs.jctc.8b01123  0.304
2019 Elofsson A, Hess B, Lindahl E, Onufriev A, van der Spoel D, Wallqvist A. Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. Plos Computational Biology. 15: e1006649. PMID 30653494 DOI: 10.1371/Journal.Pcbi.1006649  0.318
2017 Forouzesh N, Izadi S, Onufriev AV. Grid-based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies. Journal of Chemical Information and Modeling. PMID 28786669 DOI: 10.1021/acs.jcim.7b00192  0.312
2017 Katkova EV, Onufriev AV, Aguilar B, Sulimov VB. Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding. Journal of Molecular Graphics & Modelling. 72: 70-80. PMID 28064081 DOI: 10.1016/j.jmgm.2016.12.011  0.308
2016 Rychkov GN, Ilatovskiy AV, Nazarov IB, Shvetsov AV, Lebedev DV, Konev AY, Isaev-Ivanov VV, Onufriev AV. Partially Assembled Nucleosome Structures at Atomic Detail. Biophysical Journal. PMID 28038734 DOI: 10.1016/j.bpj.2016.10.041  0.307
2016 Izadi S, Anandakrishnan R, Onufriev AV. Implicit Solvent Simulation of Million-Atom Structures: Insights into the Organization of 30-nm Chromatin Fiber. Journal of Chemical Theory and Computation. PMID 27748599 DOI: 10.1021/acs.jctc.6b00712  0.324
2015 Izadi S, Aguilar B, Onufriev AV. Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation. Journal of Chemical Theory and Computation. 11: 4450-9. PMID 26575935 DOI: 10.1021/acs.jctc.5b00483  0.322
2015 Drozdetski AV, Anandakrishnan R, Onufriev A. Estimating Persistence Length of DNA from Molecular Dynamics Simulations Biophysical Journal. 108: 233a. DOI: 10.1016/J.Bpj.2014.11.1287  0.429
2014 Drozdetski A, Mukhopadhyay A, Onufriev A. Strongly Bent DNA: Reconciling Theory and Experiment Biophysical Journal. 106: 280a. DOI: 10.1016/J.Bpj.2013.11.1637  0.383
2013 Onufriev AV, Alexov E. Protonation and pK changes in protein-ligand binding. Quarterly Reviews of Biophysics. 46: 181-209. PMID 23889892 DOI: 10.1017/S0033583513000024  0.321
2013 Drozdetski A, Onufriev A. The Physics of DNA Bending Biophysical Journal. 104: 15a-16a. DOI: 10.1016/J.Bpj.2012.11.117  0.376
2011 Wang Z, Huang Y, Li L, Thomas DG, Pollack L, Onufriev A, Baker NA. Improving Electrostatic Descriptions of Ions Around Double-Stranded DNA Biophysical Journal. 100: 77a. DOI: 10.1016/J.Bpj.2010.12.627  0.347
2011 Baker CJ, Onufriev A, Mukhopadhyay B. Insights into Halophilic Protein Stability via the Generalized Born Model Biophysical Journal. 100: 47a. DOI: 10.1016/J.Bpj.2010.12.457  0.375
2011 Baker CJ, Anandakrishnan R, Onufriev A. Low Order Physical Multipoles Biophysical Journal. 100: 614a. DOI: 10.1016/J.Bpj.2010.12.3535  0.308
2010 Aguilar B, Anandakrishnan R, Ruscio JZ, Onufriev AV. Statistics and physical origins of pK and ionization state changes upon protein-ligand binding. Biophysical Journal. 98: 872-80. PMID 20197041 DOI: 10.1016/J.Bpj.2009.11.016  0.654
2008 Gordon JC, Fenley AT, Onufriev A. An analytical approach to computing biomolecular electrostatic potential. II. Validation and applications. The Journal of Chemical Physics. 129: 075102. PMID 19044803 DOI: 10.1063/1.2956499  0.377
2008 Fenley AT, Gordon JC, Onufriev A. An analytical approach to computing biomolecular electrostatic potential. I. Derivation and analysis. The Journal of Chemical Physics. 129: 075101. PMID 19044802 DOI: 10.1063/1.2956497  0.301
2008 Ruscio JZ, Kumar D, Shukla M, Prisant MG, Murali TM, Onufriev AV. Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin. Proceedings of the National Academy of Sciences of the United States of America. 105: 9204-9. PMID 18599444 DOI: 10.1073/Pnas.0710825105  0.661
2008 Onufriev A. Chapter 7 Implicit Solvent Models in Molecular Dynamics Simulations: A Brief Overview Annual Reports in Computational Chemistry. 4: 125-137. DOI: 10.1016/S1574-1400(08)00007-8  0.331
2007 Mongan J, Svrcek-Seiler WA, Onufriev A. Analysis of integral expressions for effective Born radii. The Journal of Chemical Physics. 127: 185101. PMID 18020664 DOI: 10.1063/1.2783847  0.332
2007 Saha N, Watson LT, Kafadar K, Ramakrishnan N, Onufriev A, Mane S, Vasquez-Robinet C. Validation and estimation of parameters for a general probabilistic model of the PCR process. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 97-112. PMID 17381349 DOI: 10.1089/Cmb.2006.0123  0.3
2006 Ruscio JZ, Onufriev A. A computational study of nucleosomal DNA flexibility. Biophysical Journal. 91: 4121-32. PMID 16891359 DOI: 10.1529/Biophysj.106.082099  0.634
2006 Sigalov G, Fenley A, Onufriev A. Analytical electrostatics for biomolecules: beyond the generalized Born approximation. The Journal of Chemical Physics. 124: 124902. PMID 16599720 DOI: 10.1063/1.2177251  0.371
2006 Myers J, Grothaus G, Narayanan S, Onufriev A. A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules. Proteins. 63: 928-38. PMID 16493626 DOI: 10.1002/Prot.20922  0.352
2005 Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. Journal of Computational Chemistry. 26: 1668-88. PMID 16200636 DOI: 10.1002/Jcc.20290  0.305
2005 Sigalov G, Scheffel P, Onufriev A. Incorporating variable dielectric environments into the generalized Born model. The Journal of Chemical Physics. 122: 094511. PMID 15836154 DOI: 10.1063/1.1857811  0.312
2004 Saha N, Watson LT, Kafadar K, Onufriev A, Ramakrishnan N, Vasquez-Robinet C, Watkinson J. A general probabilistic model of the PCR process. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 4: 2813-6. PMID 17270862 DOI: 10.1016/J.Amc.2006.01.092  0.313
2004 Onufriev A, Bashford D, Case DA. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins. 55: 383-94. PMID 15048829 DOI: 10.1002/Prot.20033  0.456
2004 Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL. Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. Journal of Computational Chemistry. 25: 265-84. PMID 14648625 DOI: 10.1002/Jcc.10378  0.407
2004 Onufriev A, Ullmann GM. Decomposing Complex Cooperative Ligand Binding into Simple Components:  Connections between Microscopic and Macroscopic Models The Journal of Physical Chemistry B. 108: 11157-11169. DOI: 10.1021/Jp049961G  0.41
2003 Onufriev A, Smondyrev A, Bashford D. Proton affinity changes driving unidirectional proton transport in the bacteriorhodopsin photocycle. Journal of Molecular Biology. 332: 1183-93. PMID 14499620 DOI: 10.1016/S0022-2836(03)00903-3  0.311
2003 Onufriev A, Case DA, Bashford D. Structural details, pathways, and energetics of unfolding apomyoglobin. Journal of Molecular Biology. 325: 555-67. PMID 12498802 DOI: 10.1016/S0022-2836(02)01207-X  0.427
2002 Onufriev A, Case DA, Bashford D. Effective Born radii in the generalized Born approximation: the importance of being perfect. Journal of Computational Chemistry. 23: 1297-304. PMID 12214312 DOI: 10.1002/Jcc.10126  0.327
2000 Onufriev A, Bashford D, Case DA. Modification of the Generalized Born Model Suitable for Macromolecules The Journal of Physical Chemistry B. 104: 3712-3720. DOI: 10.1021/Jp994072S  0.308
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