Alexey Onufriev - Publications

Affiliations: 
Virginia Polytechnic and State University, United States 
Area:
General Biophysics, Computer Science

63 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
2018 Anandakrishnan R, Izadi S, Onufriev AV. Why computed protein folding landscapes are sensitive to the water model. Journal of Chemical Theory and Computation. PMID 30514080 DOI: 10.1021/acs.jctc.8b00485  0.36
2018 Fenley AT, Anandakrishnan R, Kidane YH, Onufriev AV. Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core. Epigenetics & Chromatin. 11: 11. PMID 29548294 DOI: 10.1186/s13072-018-0181-5  0.36
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  0.36
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  0.36
2016 Drozdetski AV, Tolokh IS, Pollack L, Baker N, Onufriev AV. Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA. Physical Review Letters. 117: 028101. PMID 27447528 DOI: 10.1103/PhysRevLett.117.028101  1
2016 Pabit SA, Katz AM, Tolokh IS, Drozdetski A, Baker N, Onufriev AV, Pollack L. Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations. The Journal of Chemical Physics. 144: 205102. PMID 27250330 DOI: 10.1063/1.4950814  1
2016 Sushko ML, Thomas DG, Pabit SA, Pollack L, Onufriev AV, Baker NA. The Role of Correlation and Solvation in Ion Interactions with B-DNA. Biophysical Journal. 110: 315-26. PMID 26789755 DOI: 10.1016/j.bpj.2015.12.011  1
2016 Tolokh IS, Drozdetski AV, Pollack L, Baker NA, Onufriev AV. Multi-shell model of ion-induced nucleic acid condensation Journal of Chemical Physics. 144. DOI: 10.1063/1.4945382  1
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  1
2015 Kinney NA, Onufriev AV, Sharakhov IV. Quantified effects of chromosome-nuclear envelope attachments on 3D organization of chromosomes. Nucleus (Austin, Tex.). 6: 212-24. PMID 26068134 DOI: 10.1080/19491034.2015.1056441  1
2015 Mukhopadhyay A, Tolokh IS, Onufriev AV. Accurate evaluation of charge asymmetry in aqueous solvation. The Journal of Physical Chemistry. B. 119: 6092-100. PMID 25830623 DOI: 10.1021/acs.jpcb.5b00602  1
2015 Anandakrishnan R, Drozdetski A, Walker RC, Onufriev AV. Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations. Biophysical Journal. 108: 1153-64. PMID 25762327 DOI: 10.1016/j.bpj.2014.12.047  1
2014 Onufriev AV, Aguilar B. Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions. Journal of Theoretical & Computational Chemistry. 13. PMID 26236064 DOI: 10.1142/S0219633614400069  0.36
2014 Izadi S, Anandakrishnan R, Onufriev AV. Building Water Models: A Different Approach. The Journal of Physical Chemistry Letters. 5: 3863-3871. PMID 25400877 DOI: 10.1021/jz501780a  1
2014 Tolokh IS, Pabit SA, Katz AM, Chen Y, Drozdetski A, Baker N, Pollack L, Onufriev AV. Why double-stranded RNA resists condensation. Nucleic Acids Research. 42: 10823-31. PMID 25123663 DOI: 10.1093/nar/gku756  1
2014 Mukhopadhyay A, Aguilar BH, Tolokh IS, Onufriev AV. Introducing Charge Hydration Asymmetry into the Generalized Born Model. Journal of Chemical Theory and Computation. 10: 1788-1794. PMID 24803871 DOI: 10.1021/ct4010917  1
2014 Kinney NA, Sharakhov IV, Onufriev AV. Investigation of the chromosome regions with significant affinity for the nuclear envelope in fruit fly--a model based approach. Plos One. 9: e91943. PMID 24651400 DOI: 10.1371/journal.pone.0091943  1
2014 Onufriev AV, Aguilar B. Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions Journal of Theoretical and Computational Chemistry. 13. DOI: 10.1142/S0219633614400069  1
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  1
2013 Anandakrishnan R, Baker C, Izadi S, Onufriev AV. Point charges optimally placed to represent the multipole expansion of charge distributions. Plos One. 8: e67715. PMID 23861790 DOI: 10.1371/journal.pone.0067715  1
2013 Savin AV, Kikot IP, Mazo MA, Onufriev AV. Two-phase stretching of molecular chains. Proceedings of the National Academy of Sciences of the United States of America. 110: 2816-21. PMID 23378631 DOI: 10.1073/pnas.1218677110  1
2012 Aguilar B, Onufriev AV. Efficient Computation of the Total Solvation Energy of Small Molecules via the R6 Generalized Born Model. Journal of Chemical Theory and Computation. 8: 2404-11. PMID 26588972 DOI: 10.1021/ct200786m  0.36
2012 Mukhopadhyay A, Fenley AT, Tolokh IS, Onufriev AV. Charge hydration asymmetry: the basic principle and how to use it to test and improve water models. The Journal of Physical Chemistry. B. 116: 9776-83. PMID 22762271 DOI: 10.1021/jp305226j  1
2012 Anandakrishnan R, Aguilar B, Onufriev AV. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Research. 40: W537-41. PMID 22570416 DOI: 10.1093/nar/gks375  1
2012 Aguilar B, Onufriev AV. Efficient computation of the total solvation energy of small molecules via the r6 generalized born model Journal of Chemical Theory and Computation. 8: 2404-2411. DOI: 10.1021/ct200786m  1
2011 Anandakrishnan R, Daga M, Onufriev AV. An n log n Generalized Born Approximation. Journal of Chemical Theory and Computation. 7: 544-59. PMID 26596289 DOI: 10.1021/ct100390b  1
2011 Savin AV, Mazo MA, Kikot IP, Manevitch LI, Onufriev AV. Heat conductivity of DNA double helix. Physical Review. B, Condensed Matter and Materials Physics. 83. PMID 26207085 DOI: 10.1103/PhysRevB.83.245406  1
2011 Kikot' IP, Savin AV, Zubova EA, Mzo MA, Gusarova EB, Manevich LI, Onufriev AV. [New coarse-grained DNA model] Biofizika. 56: 396-402. PMID 21786691  1
2011 Onufriev AV, Sigalov G. A strategy for reducing gross errors in the generalized Born models of implicit solvation. The Journal of Chemical Physics. 134: 164104. PMID 21528947 DOI: 10.1063/1.3578686  1
2011 Kikot IP, Savin AV, Zubova EA, Mazo MA, Gusarova EB, Manevitch LI, Onufriev AV. New coarse-grained DNA model Biophysics. 56: 387-392. DOI: 10.1134/S0006350911030109  1
2010 Fenley AT, Adams DA, Onufriev AV. Charge state of the globular histone core controls stability of the nucleosome. Biophysical Journal. 99: 1577-85. PMID 20816070 DOI: 10.1016/j.bpj.2010.06.046  1
2010 Anandakrishnan R, Scogland TR, Fenley AT, Gordon JC, Feng WC, Onufriev AV. Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units. Journal of Molecular Graphics & Modelling. 28: 904-10. PMID 20452792 DOI: 10.1016/j.jmgm.2010.04.001  1
2010 Palpant NJ, Houang EM, Delport W, Hastings KE, Onufriev AV, Sham YY, Metzger JM. Pathogenic peptide deviations support a model of adaptive evolution of chordate cardiac performance by troponin mutations. Physiological Genomics. 42: 287-99. PMID 20423961 DOI: 10.1152/physiolgenomics.00033.2010  1
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  1
2010 Anandakrishnan R, Onufriev AV. An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions. Journal of Computational Chemistry. 31: 691-706. PMID 19569183 DOI: 10.1002/jcc.21357  1
2010 Aguilar B, Shadrach R, Onufriev AV. Reducing the secondary structure bias in the generalized Born model via R6 effective radii Journal of Chemical Theory and Computation. 6: 3613-3630. DOI: 10.1021/ct100392h  1
2010 Onufriev A. Continuum Electrostatics Solvent Modeling with the Generalized Born Model Modeling Solvent Environments: Applications to Simulations of Biomolecules. 127-165. DOI: 10.1002/9783527629251.ch6  1
2009 Bhattacharjee P, Ramakrishnan N, Heath LS, Onufriev AV. Correlation between computed equilibrium secondary structure free energy and siRNA efficiency Proceedings - 2009 Ieee International Conference On Bioinformatics and Biomedicine Workshops, Bibmw 2009. 358. DOI: 10.1109/BIBMW.2009.5332077  1
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  1
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  1
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  1
2008 Anandakrishnan R, Onufriev A. Analysis of basic clustering algorithms for numerical estimation of statistical averages in biomolecules. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 165-84. PMID 18312148 DOI: 10.1089/cmb.2007.0144  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2005 Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, Onufriev A. H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Research. 33: W368-71. PMID 15980491 DOI: 10.1093/nar/gki464  1
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  1
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: 10.1109/IEMBS.2004.1403803  1
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  1
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  1
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  1
2003 Allawi HT, Kaiser MW, Onufriev AV, Ma WP, Brogaard AE, Case DA, Neri BP, Lyamichev VI. Modeling of flap endonuclease interactions with DNA substrate. Journal of Molecular Biology. 328: 537-54. PMID 12706715 DOI: 10.1016/S0022-2836(03)00351-6  1
2003 Hirst JD, Bhattacharjee S, Onufriev AV. Theoretical studies of time-resolved spectroscopy of protein folding. Faraday Discussions. 122: 253-67; discussion 2. PMID 12555862 DOI: 10.1039/b200714b  1
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  1
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  1
2001 Onufriev A, Case DA, Ullmann GM. A novel view of pH titration in biomolecules Biochemistry. 40: 3413-3419. PMID 11297406 DOI: 10.1021/bi002740q  1
2000 Onufriev A, Bashford D, Case DA. Modification of the generalized born model suitable for macromolecules Journal of Physical Chemistry B. 104: 3712-3720.  1
1999 Onufriev AV, Marston JB. Enlarged symmetry and coherence in arrays of quantum dots Physical Review B - Condensed Matter and Materials Physics. 59: 12573-12578.  1
1996 Onufriev AV, Marston JB. Memory loss and Auger processes in a many-body theory of charge transfer Physical Review B - Condensed Matter and Materials Physics. 53: 13340-13356.  1
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