Home Research Lab members Teaching Publications Software Molecular biophysics Publications. As of 09/2024, the total number of citations is 31000. Source: Google Scholar. 103. Egor S. Kolesnikov, Yeyue Xiong, and Alexey V. Onufriev, ``Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA", Journal of Chemical Theory and Computation, (2024). 102. IS Tolokh, DE Folescu, and Alexey V. Onufriev, ``Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains", 128, 5855–5873 (2024). 101. Alexander Y. Afanasyev, Yoonjin Kim, Igor S. Tolokh, Igor V. Sharakhov, and Alexey V. Onufriev, ``The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit fly", Epigenetics & Chromatin, 17, Article number: 13 (2024) . 100. Lewis Bass, Luke H Elder, Dan E Folescu, Negin Forouzesh, Igor S Tolokh, Anuj Karpatne, Alexey V. Onufriev, ``Improving the Accuracy of Physics-Based Hydration-Free Energy Predictions by Machine Learning the Remaining Error Relative to the Experiment", Journal of Chemical Theory and Computation, 20, 396–410 (2024). 99. David A Case, ... Alexey V. Onufriev.... et al. , ``AmberTools", J. Chem. Inf. Model. 63, 20, 6183–6191 (2023). 98. ES Kolesnikov, IY Guschin, PA Zhilyaev, and Alexey V. Onufriev, ``Why Na+ has higher propensity than K+ to condense DNA in a crowded environment", J. Chem. Phys., 159, 145103 (2023). 97. IS Tolokh, NA Kinney, IV Sharakhov, Alexey V. Onufriev, ``Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin", Epigenetics and Chromatin 16, 1-25 (2023). 96. Alexey V. Onufriev, ``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 (2023). 95. Yeyue Xiong, Saeed Izadi, and Alexey V. Onufriev, ``Fast Polarizable Water Model for Atomistic Simulations", Journal of Chemical Theory and Computation, 18, 6324–6333 (2022). 94. D. E. Folescu and Alexey V. Onufriev, ``A closed-form, analytical approximation for apparent surface charge and electric field of molecules", ACS Omega, 7, 26123-26136 (2022). 93. AY Afanasyev and Alexey V. Onufriev, “Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach”, Journal of Chemical Theory and Computation, 18, 3911-3920 (2022). 92. ES Kolesnikov, IY Gushchin, PA Zhilyaev and Alexey V. Onufriev, ``Similarities and Differences between Na+ and K+ Distributions around DNA Obtained with Three Popular Water Models", Journal of Chemical Theory and Computation 17, 7246-7259 (2021). 91. KS Onufrieva and Alexey V. Onufriev, ``How to Count Bugs: A Method to Estimate the Most Probable Absolute Population Density and Its Statistical Bounds from a Single Trap Catch", Insects 12, 932 (2021). 90. Y Peng, S Li, Alexey V. Onufriev, D. Landsman, Anna R. Panchenko, ``Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails", Nature communications 12, 1-12 (2021). 89. Parviz Shabane and Alexey V. Onufriev, ``Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure", Journal of Molecular Biology, 433, 166683 (2021). 88. KS Onufrieva, Alexey V. Onufriev, AD Hickman, JR Miller, ``Bounds on Absolute Gypsy Moth (Lymantria dispar dispar)(Lepidoptera: Erebidae) Population Density as Derived from Counts in Single Milk Carton Traps", Insects 11, 673 (2020). 87. Negin Forouzesh and Alexey V. Onufriev, ``MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor", bioRxiv, 10.1101/2020.08.25.267625 (2020). 86. Yeyue Xiong, Parviz Shabane and Alexey V. Onufriev ``Melting points of OPC and OPC3 water models", ACS Omega (2020). 85. N Forouzesh, A Mukhopadhyay, LT Watson, Alexey V. Onufriev, ``Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding", J. Chem. Theory Comput. 16, 4669–4684 (2020). 84. N Forouzesh, LT Watson, Alexey V. Onufriev, ``Robustness of multidimensional optimization outcomes: a general approach and a case study", Proceedings of the Spring Simulation Conference, 1-12 (2020). 83. P George, NA Kinney, J Liang, AV Onufriev, IV Sharakhov, ``Three-dimensional Organization of Polytene Chromosomes in Somatic and Germline Tissues of Malaria Mosquitoes", Cells 9, 339 (2020). 82. Yeyue Xiong and Alexey V. Onufriev, ``Exploring optimization strategies for improving explicit water models: Rigid n-point model and polarizable model based on Drude oscillator", Plos One, 14, e0224991 (2019). 81. Aleksander V. Drozdetski, Abhishek Mukhopadhyay and Alexey V. Onufriev, ``Strongly bent double-stranded DNA: reconciling theory and experiment", Frontiers in Physics 7, 195 (2019). 80. Parviz S. Shabane, Saeed Izadi, and Alexey V. Onufriev, ``General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins", Journal of Chemical Theory and Computation 15, 2620-2634 (2019). 79. Alexey V. Onufriev and David A. Case, ``Generalized Born Implicit Solvent Models for Biomolecules", Annual review of biophysics 48, 275-296 (2019). 78. Alexey V. Onufriev and Helmut Schiessel, ``The nucleosome: from structure to function through physics", Current opinion in structural biology 56, 119-130 (2019). 77. Arne Elofsson, Berk Hess, Erik Lindahl, Alexey V. Onufriev, David van der Spoel, Anders Wallqvist, ``Ten simple rules on how to create open access and reproducible molecular simulations of biological systems", PLoS computational biology, 15, e1006649 (2019). 76. Ramu Anandakrishnan, Saeed Izadi, Alexey V. Onufriev ``Why computed protein folding landscapes are sensitive to the water model", Journal of Chemical Theory and Computation 15, 625-636 (2019). 75. Igor S. Tolokh, Dennis G. Thomas, and Alexey V. Onufriev, ``Explicit ions/implicit water generalized Born model for nucleic acids", The Journal of Chemical Physics, 148,195101 (2018). 74. Andrew T. Fenley, Ramu Anandakrishnan, Yared Kidaine, and Alexey V. Onufriev, ``Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core", Epigenetics & Chromatin 11, 11 (2018). 73. I. V. Sharakhov, S. M. Bondarenko, G. N. Artemov, and A. V. Onufriev, "The Role of Chromosome–Nuclear Envelope Attachments in 3D Genome Organization" Biochemistry (Moscow), 83, 494-504 (2018). 72. K.S. Onufrieva, Alexey V. Onufriev ``Linear relationship between peak and season-long abundances in insects", Plos One, 13, e0193110 (2018). 71. Nicholas A. Kinney, Igor V. Sharakhov, and Alexey V. Onufriev ``Chromosome–nuclear envelope attachments affect interphase chromosome territories and entanglement", Epigenetics and Chromatin, 11, 3, (2018). 70. Alexey V. Onufriev, and Saeed Izadi ``Water models for biomolecular simulations", WIREs Computational Molecular Science, 8, e1347, (2018). 69. Saeed Izadi, Robert C. Harris, Marcia O. Fenley, and Alexey V. Onufriev ``Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies", Journal of Chemical Theory and Comoutation, (2018). 68. Negin Forouzesh, Saeed Izadi, and Alexey V. Onufriev ``Grid-based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies", Journal of Chemical Information and Modeling, 57, 2505-2513 (2017). 67. A. Gabrieli, M. Sant, S. Izadi, P.S. Shabane, A.V. Onufriev, G.B. Suffritti ``High-Temperature Dynamic Behavior in Bulk Liquid Water: A Molecular Dynamics Simulation Study using the OPC and TIP4P-Ew Potentials", Frontiers of Physics 13, 138203 (2018). 66. Ekaterina Katkova, Alexey V. Onufriev, Boris Aguilar, and Vladimir B. Sulimov ``Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding", Journal of Molecular Graphics and Modelling, 72, 70-80 (2017). 65. Andrea M Katz, Igor S Tolokh, Suzette A Pabit, Nathan Baker, Alexey V Onufriev, Lois Pollack ``Spermine condenses DNA, but not RNA duplexes", Biophysical Journal, 112, 22-30, (2017). 64. Ramu Anandakrishnan, Mayank Daga, Alexey Onufriev, and Wu Feng ``Multiscale Approximation with Graphical Processing Units for Multiplicative Speedup in Molecular Dynamics", Proceedings of the 7th ACM Conference on Buoinformatics, Computational Biology, and Health Informatics, Seattle, WA, October (2016). 63. Georgy N. Rychkov, Andrey V. Ilatovskiy, Igor Nazarov, Alexei Shvetsov, Dmitry Lebedev, Alexander Konev, Vladimir Isaev-Ivanov, and Alexey. V. Onufriev “Partially assembled nucleosome structures at atomic detail", Biophysical Journal, 112, 46-472, (2016). 62. Saeed Izadi, Ramu Anandakrishnan*, and Alexey V. Onufriev “Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber", Journal of Chemical Theory and Computation, 12, pp 5946–5959, (2016). 61. Saeed Izadi and A.V. Onufriev ``Accuracy Limit of Rigid 3-point Water Models", J. Chem. Phys., 145, 074501 (2016). 60. Alexander Drozdetski, Igor S. Tolokh, Lois Pollack, Nathan Baker , and Alexey V. Onufriev, “Opposing effects of multivalent ions on flexibility of DNA and RNA”, Physical Review Letters, 117, 028101 (2016). 59. Suzette A Pabit, Andrea M Katz, Igor S Tolokh, Aleksander Drozdetski, Nathan Baker, Alexey V Onufriev, Lois Pollack ``Understanding Nucleic Acid Structural Changes by Comparing Wide-Angle X-ray Scattering (WAXS) Experiments to Molecular Dynamics Simulations", J. Chem. Phys. 144, 205102 (2016). 58. I.S. Tolokh, A.V. Drozdetski, L. Pollack, N.A. Baker, and A.V. Onufriev ``Multi-shell model of ion-induced nucleic acid condensation", J. Chem. Phys., 144, 155101 (2016). 57. Maria L. Sushko, Dennis G. Thomas, Suzette A. Pabit, Lois Pollack, Alexey V. Onufriev, Nathan A. Baker ``The Role of Correlation and Solvation in Ion Interactions with B-DNA", Biophysical Journal, 110, 315-326 (2016). 56. Saeed Izadi, Boris Aguilar, Alexey V. Onufriev ``Protein–Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation", J. Chem. Theory and Comput., 11, 4450-4459 (2015). 55. Nicholas A. Kinney, Igor Sharakhov, and Alexey V. Onufriev ``Quantified effects of chromosome-nuclear envelope attachments on 3D organization of chromosomes", Nucleus, 6, 212-224 (2015). 54. Abhishek Mukhopadhyay, Igor S. Tolokh, and Alexey V. Onufriev ``Accurate Evaluation of Charge Asymmetry in Aqueous Solvation", Journal of Physical Chemistry (B) 119, 6092–6100 (2015). 53. Ramu Anandakrishnan, Aleksander Drozdetski, Ross Walker, and Alexey V. Onufriev ``Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations", Biophysical Journal 108, 1153-64 (2015). 52. Saeed Izadi, Ramu Anandakrishnan and Alexey V. Onufriev ``Building Water Models, a Different Approach", J. Phys. Chem. Lett. 5, 3863-3871 (2014). 51. Igor S. Tolokh, Suzette A. Pabit, Andrea M. Katz, Yujie Chen, Aleksander Drozdetski, Nathan Baker, Lois Pollack, and Alexey V. Onufriev ``Why double-stranded RNA resists condensation", Nucleic Acids Research, 42, 10823-10831 (2014). 50. Abhishek Mukhopadhyay, Boris Aguilar, Igor S. Tolokh, and Alexey V. Onufriev ``Introducing Charge Hydration Asymmetry into the Generalized Born Model", J. Chem. Theory and Comput., 10 1788–1794 (2014). 49. Alexey V. Onufriev and Boris Aguilar ``Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions.", J. Theor. and Comput. Chemistry, 13, 1440006 (2014). 48. Nicholas A. Kinney, Igor Sharakhov, and Alexey V. Onufriev. "Investigation of the chromosome regions with significant affinity for the nuclear envelope in fruit fly – a model based approach", PLOS One, 9, e91943 (2014). 47. Anandakrishnan R, Baker C, Izadi S, Onufriev AV. ``Point Charges Optimally Placed to Represent the Multipole Expansion of Charge Distributions, PLOS One, 8, e6771 (2013). 46. Alexey V. Onufriev and Emil Alexov. ``Protonation and pK changes in protein-ligand binding", Quarterly Review of Biophysics, 46, 181-209 (2013). 45. Alexander V. Savin, Mikhail A. Mazo, Irina P. Kikot, and Alexey V. Onufriev. ``Two-phase stretching of molecular chains", Proceedings of the National Academy of Sciences, USA, 110, 2816-2821 (2013). 44. B. Aguilar and A.V. Onufriev. ``Efficient Computation of the Total Solvation Energy of Small Molecules via the R6 Generalized Born Model". J. Chem. Theory and Comput., 8, 2404-2411 (2012). 43. Abhishek Mukhopadhyay, Andrew T. Fenley, Igor S. Tolokh, and Alexey V. Onufriev. ``Charge Hydration Asymmetry: The Basic Principle and How to Use It to Test and Improve Water Models". Journal of Physical Chemistry (B), 116 9776–9783 (2012). 42. Ramu Anandakrishnan, Boris Aguilar and Alexey V. Onufriev. ``H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulation". Nucleic Acids Research, 40(W1), 537-541 (2012). 41. I.P Kikot, A.V. Savin, E.A. Zubova, M.A. Mazo, E.B. Gusarova, L.I. Manevitch, and A.V. Onufriev. ``New Coarse-Grained DNA Model", Biophysics, 56, 387-392 (2011). 40. Alexander V. Savin, Mikhail A. Mazo, Irina P. Kikot, Leonid I. Manevitch, and Alexey V. Onufriev. ``Heat conductivity of the DNA double helix", Phys. Rev. B 83, 245406 (2011). 39. Onufriev, A. V., and Sigalov, G. ``A strategy for reducing gross errors in the generalized Born models of implicit solvation", The Journal of Chemical Physics, 134, 164104, (2011). 38. Ramu Anandakrishnan, Mayank Daga, and Alexey V. Onufriev. ``An n log n Generalized Born Approximation", J. Chem. Theory and Comput. 7, 544-559 (2011). 37. Boris Aguilar, Richard Shadrach, and Alexey V. Onufriev. ``Reducing the Secondary Structure Bias in the Generalized Born Model via R6 Effective Radii", J. Chem. Theory and Comput., 6, 3613–3630 (2010). 36. Andrew T. Fenley, David A. Adams, and Alexey V. Onufriev. ``Charge State of the Globular Histone Core Controls Stability of the Nucleosome" Biophysical Journal, 99, 1577-1585 (2010). 35. 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", J. Mol. Graph. Model., 28, 904-910 (2010). 34. Nathan J. Palpant, Evelyne M. Houang, Wayne Delport, Kenneth E. M. Hastings, Alexey V. Onufriev, Yuk Y. Sham, and Joseph M. Metzger. ``Pathogenic peptide deviations support a model of adaptive evolution of chordate cardiac performance by troponin mutations", Physiol. Genomics, 42, 287-299, (2010). 33. Onufriev, Alexey. ``Continuum Electrostatics Solvent Modeling with the Generalized Born Model", pp. 127--165. In: Modeling Solvent Environments. Editor: M. Feig. Publisher: Wiley (2010). 32. 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, 872-880 (2010). 31. Ramu Anandakrishnan and Alexey V. Onufriev, ``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 (2010). 30. Bhattacharjee, P., N. Ramakrishnan, L. S. Heath, and A. V. Onufriev, ``Correlation Between Computed Equilibrium Secondary Structure Free Energy and siRNA Efficiency", IEEE International Conference on Bioinformatics and Biomedicine, Washington, DC, 351–351, (2009) 29. A. Onufriev, ``Implicit Solvent Models in Molecular Dynamics Simulations", Annual Reports in Computational Chemistry, 4, 125-137 (2008). PDF 28. John C. Gordon, Andrew T. Fenley, and A. Onufriev, ``An Analytical Approach to Computing Biomolecular Electrostatic Potential, II: Validation and Applications", Journal of Chemical Physics, 129, 075102 (2008). PDF 27. Andrew T. Fenley, John C. Gordon, and A. Onufriev, ``An Analytical Approach to Computing Biomolecular Electrostatic Potential, I: Derivation and Analysis", Journal of Chemical Physics, 129, 075101 (2008). PDF 26. Jory Z. Ruscio, Deept Kumar, Maulik Shukla, Michael G. Prisant, T. M. Murali, and Alexey V. Onufriev, ``Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin", Proceedings of the National Academy of Sciences, (USA), 15, 9204-9209 (2008). 25. Ramu Anandakrishnan and Alexey Onufriev, ``Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules", Journal of Computational Biology, 15, 165-184 (2008). 24. J. Mongan, A. Svrcek-Seiler, and A. Onufriev, ``Analysis of integral expressions for effective Born radii", J. Chem. Phys. 127, 185101 (2007). PDF 23. J. Mongan, C Simmerling, J.A. McCammon, D.A. Case, and A. Onufriev, `` Generalized Born Model with a Simple, Robust Molecular Volume Correction ", J. Chem. Theory and Comput., 3, 156-169 (2007). PDF 22. N. Saha, L. T. Watson, K. Kafadar, N. Ramakrishnan, A. Onufriev, S. P. Mane, and C. Vasquez-Robinet, "Validation and estimation of parameters for a general probabilistic model of the PCR process'', J. Comput. Biology, 14, 102--117 (2007) 21. J. Z. Ruscio and Alexey Onufriev, "A Computational Study of Nucleosomal DNA Flexibility", Biophys. J., 91, 4121-4132 (2006). PDF 20. N. Saha, L. T. Watson, K. Kafadar, A. Onufriev, N. Ramakrishnan, C. Vasquez-Robinet, and J. Watkinson, ``A general probabilistic model of the PCR process'', Appl. Math. Comput., 182, 232--243, (2006) 19. 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, 928-938 (2006). PDF 18. G. Sigalov, A. Fenley, and A. Onufriev, "Analytical Linearized Poisson--Boltzmann Approach: Beyond the Generalized Born Approximation", J. Chem. Phys., 124, 124902 (2006). PDF 17. David A. Case, Thomas E. Cheatham III, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz Jr., Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods, "The Amber biomolecular simulation programs", J. Comp. Chem., 26, 1668-1688 (2005). PDF 16. Gordon JC, Myers JB, Folta T, Shoja V, Heath LS and Onufriev A., "H++: a server for estimating pKas and adding missing hydrogens to macromolecules", Nucleic Acids Res. Jul 1;33:W368-71. (2005). PDF 15. G. Sigalov, P. Scheffel, and A. Onufriev, "Incorporating variable dielectric environments into the generalized Born model", J. Chem. Phys., 122, (2005). PDF 14. A. Onufriev and G. M. Ullmann, "Decomposing Complex Ligand Binding into Simple Components: Connections between Microscopic and Macroscopic models", J. Phys. Chem. B., 108, 11157-11169 (2004). PDF 13. M. Feig, A. Onufriev, M. S. Lee, W. Im, D. A. Case, C. L. Brooks, ``Performance Comparison of Generalized Born and Poisson Methods in the Calculation of Electrostatic Solvation Energies for Protein Structures", J. Comp. Chem , 468 , 96-111 (2004). PDF 12. Alexey Onufriev, D. Bashford and D.A. Case, "Exploring native states and large-scale conformational changes with a modified Generalized Born model.", Proteins, 55, 383-394 (2004). PDF 11. Alexey Onufriev, A. Smondyrev, and D. Bashford, ``Proton Affinity Changes Driving Unidirectional Proton Transport in the Bacteriorhodopsin Photocycle", J. Mol. Biol. 232 , 1183-1193 (2003). PDF 10. H. T. Allawi, M. W. Kaiser, Alexey Onufriev, Wu-Po Ma, A. E. Brogaard, D. A. Case, B. P. Neri and V. I. Lyamichev, "Modeling of Flap Endonuclease Interactions with DNA Substrate", J. Mol. Biol. 328 , 537-554 (2003). PDF 9. J. D. Hirst, S. Bhattacharjee, and Alexey Onufriev, Theoretical studies of time-resolved spectroscopy of protein folding", Faraday Discussions. 122, 253-267 (2003). PDF 8. Alexey Onufriev, D.A. Case, and D. Bashford, "Structural details, pathways, and energetics of unfolding apomyoglobin.``, J. Mol. Biol. 325, 555-567 (2003). PDF 7. Alexey Onufriev, D. Bashford and D.A. Case, "Effective Born radii in the generalized Born approximation: The Importance of Being Perfect.", J. Comp. Chem. 23, 1297-1304 (2002). PDF 6. Alexey Onufriev, D.A. Case and G. M. Ullmann, `` A Novel View of pH Titration in Biomolecules", Biochemistry, (``New Concepts") 40, 3413 (2001). PDF 5. Leduc SA, McAuley GA, Pentzell CB, Onufriev A, Lupton JH, Asllani I, Martin T. ``Physics passages and questions." In: MCAT in-class passage compendium. The Princeton Review: (2001). (textbook) 4. Alexey Onufriev, D. Bashford and D.A. Case ``A Modification of the Generalized Born Model Suitable for Macromolecules", J. Phys. Chem., 104, 3712 (2000). PDF 3. Alexey Onufriev and J.B. Marston, ``Enlarged Symmetry and Coherence in Arrays of Quantum Dots", Phys. Rev. B., 59, 12573 (1999). PDF 2. Alexey Onufriev and J.B. Marston, ``Memory Loss and Auger Processes in a Many-Body Theory of Charge Transfer", Phys. Rev. B. 53, 13340 (1996). PDF 1. Goldfeld, M.G, Lobysheva, I., Mikoyan, M.D., Chernavskii, D.S., and Onufriev A.V., ``ATP Synthesis By Free and Membrane-Bound H+ ATPase of the Chloroplasts in Conditions of a pH shift.", Biophysics 38, 1005 (1993). ABSTRACT