Lab members
Molecular biophysics
Refereed publications. As of 11/16, the total number of citations is 9500. Source: Google Scholar.
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 (in press, 2016).
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 (in press, 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, (in press, 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. Chem. Phys. 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