 | Alexey V OnufrievAssociate Professor, Computer Science and Physics
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Research Interests
Alexey Onufriev is an associate professor in the Department of Computer Science at Virginia Tech. He also holds affiliate appointments in the Department of Physics and the GBCB (genetics, bioinformatics and computational biology) graduate program.
Alexey's research group develops and uses computational methods to understand dynamics and function of large biomolecular systems such as proteins, DNA, and their complexes. Alexey received his Ph.D. in Physics from Brown University.
Structural Bioinformatics and Computational Molecular BiophysicsContact: Alexey OnufrievOur group uses computational methods to understand dynamics and function of large biomolecular systems such as proteins, DNA, and their complexes. Some of these methods are being developed in our lab. The computations are often performed on supercomputers such as VT's System-X.
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2013
Savin, A. V., I. P. Kikot, M. A. Mazo, and A. V. Onufriev,
"Two-phase stretching of molecular chains",
Proceedings of the National Academy of Sciences, vol. 110, issue 8, pp. 2816 - 2821, 02/2013.
2012
Aguilar, B., and A. V. Onufriev,
"Efficient Computation of the Total Solvation Energy of Small Molecules via the R6 Generalized Born Model",
Journal of Chemical Theory and Computation, vol. 8, issue 7, pp. 2404 - 2411, 07/2012.
Anandakrishnan, R., B. Aguilar, and A. V. Onufriev,
"H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations",
Nucleic Acids Research, vol. 40, issue W1, pp. W537 - W541, 07/2012.
Mukhopadhyay, A., A. T. Fenley, I. S. Tolokh, and A. V. Onufriev,
"Charge Hydration Asymmetry: The Basic Principle and How to Use It to Test and Improve Water Models",
The Journal of Physical Chemistry B, vol. 116, issue 32, pp. 9776 - 9783, 08/2012.
2011
Onufriev, A. V., and G. Sigalov,
"A strategy for reducing gross errors in the generalized Born models of implicit solvation",
The Journal of Chemical Physics, vol. 134, issue 16, pp. 164104, 2011.
Anandakrishnan, R., M. Daga, and A. V. Onufriev,
"An n log n Generalized Born Approximation",
Journal of Chemical Theory and Computation, vol. 7, issue 3, pp. 544 - 559, 03/2011.
Savin, A., M. Mazo, I. Kikot, L. Manevitch, and A. Onufriev,
"Heat conductivity of the DNA double helix",
Physical Review B, vol. 83, issue 24, 6/2011.
Kikot, I. P., 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, vol. 56, issue 3, pp. 387 - 392, 6/2011.
Savin, A. V., M. A. Mazo, I. P. Kikot, L. I. Manevitch, and A. V. Onufriev,
"Heat conductivity of the DNA double helix",
Physical Review B, vol. 83, issue 24, 6/2011.
2010
Fenley, A. T., D. A. Adams, and A. V. Onufriev,
"Charge State of the Globular Histone Core Controls Stability of the Nucleosome",
Biophysical Journal, vol. 99, issue 5, pp. 1577 - 1585, 09/2010.
Aguilar, B., R. Shadrach, and A. V. Onufriev,
"Reducing the Secondary Structure Bias in the Generalized Born Model via R6 Effective Radii",
Journal of Chemical Theory and Computation, vol. 6, issue 12, pp. 3613 - 3630, 12/2010.
Anandakrishnan, R., and A. V. Onufriev,
"An NlogN approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions",
Journal of Computational Chemistry, vol. 31, no. 4, pp. 691–706, 2010.
Onufriev, A.,
"Continuum Electrostatics Solvent Modeling with the Generalized Born Model",
Modeling Solvent Environments, Weinheim, Germany, Wiley-VCH Verlag GmbH & Co. KGaA, pp. 127 - 165, 2010.
Anandakrishnan, R., T. R. W. Scogland, A. T. Fenley, J. C. Gordon, W. - C. Feng, and A. V. Onufriev,
"Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units",
Journal of Molecular Graphics and Modelling, vol. 28, issue 8, pp. 904 - 910, 06/2010.
Aguilar, B., R. Anandakrishnan, J. Z. Ruscio, and A. V. Onufriev,
"Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding",
Biophysical Journal, vol. 5, pp. 872–880, 2010.
Palpant, N., E. Houang, W. Delport, K. Hastings, A. Onufriev, Y. Sham, and J. Metzger,
"Pathogenic peptide deviations s support a model of adaptive evolution of chordate cardiac performance by troponin mutations",
Physiological Genomics, vol. 42, pp. 287-299, 07/2010.
2009
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 Workshop, Washington, DC, pp. pp. 351–351, 2009.
E.Zubova, M.Mazo, A.Savin, and I. Kikot,
"Coarse-grained model for analysis of structural transitions in DNA molecule",
In proceedings of XVI National Conference on Structure and dynamics of molecular systems: Yalchik, pp. 19-24, 2009.
Zubova, E., M.Mazo, A. Savin, I. Kikot, N. Kovaleva, E. Gusarova, L.Manevitch, and A. Onufriev,
"DNA intramolecular mobility as basis for constructing new coarse-grained model",
In: Book of abstracts of XXXVII Summer School - Conference, St. Petersburg, 06/2009.
E.Zubova, M. Mazo, A.Savin, I. Kikot, N. Kovaleva, E. Gusarova, L.Manevitch, and A. Onufriev,
"New coarse-grained DNA model",
Abstracts of the First Russian conference on Problems of mechanics and acoustics of micro- and nano-structure, Nizhniy Novgorod, 09/2009.
2008
Anandakrishnan, R., and A. Onufriev,
"Analysis of basic clustering algorithms for nu- merical estimation of statistical averages in biomolecules",
J. Comp. Biol., vol. 15, pp. 165–18, 2008.
Onufriev, A.,
"Implicit Solvent Models inMolecular Dynamics Simulations",
Annual Review of Computational Chemistry, 2008.
Fenley, A. T., J. C. Gordon, and A. Onufriev,
"An analytical approach to computing biomolecular electrostatic potential. I. Derivation and analysis",
The Journal of Chemical Physics, vol. 129, issue 7, pp. 075101, 2008.
Gordon, J. C., A. T. Fenley, and A. Onufriev,
"An analytical approach to computing biomolecular electrostatic potential. II. Validation and applications",
The Journal of Chemical Physics, vol. 129, issue 7, pp. 075102, 2008.
Z. Ruscio, J., D. Kumar, M. Shukla, M. G. Prisant, T. M. Murali, and A. Onufriev,
"Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin",
Proceedings of the National Academy of Sciences, vol. 105, no. 27, pp. 9204-9209, 2008.
Abstract
2007
Mongan, J., A. Svrcek-Seiler, and A. Onufriev,
"Analysis of integral expressions for effective Born radii",
J. Chem. Phys., vol. 127, 2007.
Mongan, J., 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, vol. 3, pp. 156-169, 2007.
Saha, N., 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. Comp. Biol., vol. 14, pp. 102–117, 2007.
Fenley, A. T., J. C. Gordon, and A. Onufriev,
"An Analytical Approach to Computing Biomolecular Electrostatic Potential",
J. Chem. Phys, 2007.
2006
Ruscio, J. Z., and A. Onufriev,
"A computational study of nucleosomal DNA flexibility",
Bio- phys J , vol. 91, pp. 4121-4132, 2006.
Saha, N., 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, vol. 182 , pp. 232–243, 2006.
Sigalov, G., A. Fenley, and A. Onufriev,
"Analytical Linearized Poisson–Boltzmann Ap- proach: Beyond the Generalized Born Approximation",
J. Chem. Phys., vol. 124, 2006.
Myers, J., G. Grothaus, and A. Onufriev,
"A simple, robust approach to calculat- ing partition function of protonation microstates in biomolecules.",
Proteins: Structure, Function, and Bioinformatics, vol. 63, pp. 928 - 938 , 2006.
2005
John C. Gordon, J. B. Myers, T. Folta, V. Shoja, L. S. Heath, and A. Onufriev,
"H++: A Server for Estimating pK(a)s and Adding Missing Hydrogens to Macromolecules",
Nucleic Acids Research , vol. 33, no. 2, pp. pp. W368-W371, 2005.
Case, D. A., T. Darden, T. Cheatham, H. Gohlke, K. Merz, A. Onufriev, R. Luo, and R. Woods,
"The Amber Bio-molecular Simulation Programs",
Journal of Computational Chemistry , vol. 26, pp. 1668-1688, 2005.
Sigalov, G., P. Scheffel, and A. Onufriev,
"Incorporating various dielectric environments into the generalized Born model",
J. Chem. Phys., vol. 122, 2005.
Onufriev, A., and G. M. Ullmann,
"Decomposing Complex Ligand Binding into Simple Com- ponents: Connections between Microscopic and Macroscopic models.",
J. Phys. Chem. , vol. 108, pp. 11157–11169, 2005.
2004
Onufriev, A., D. Bashford, and D. A. Case,
"Exploring protein native states and large-scale conformational changes with a modified Generalized Born model",
Proteins, vol. 55, pp. 383-394, 2004.
Feig, M., A. Onufriev, M. S. Lee, W. Im, D. A. Case, and C. L. Brooks.,
"Performance Comparison of Generalized Born and Poisson Methods in the Calculation of Electrostatic Solvation Energies for Protein Structures",
Journal of Computational Chemistry , vol. 468, pp. 96–111, 2004.
2003
Allawi, H. T., M. W. Kaiser, A. Onufriev, W. - P. Ma, A. E. Brogaard, D. A. Case, B. P. Neri, and V. I. Lyamichev,
"Modeling of Flap Endonuclease Interactions with DNA Substrate.",
Journal of Molecular Biology, vol. 328, pp. 537–554, 2003.
Onufriev, A., D. A. Case, and D. Bashford,
"Structural details, pathways, and energetics of unfolding apomyoglobin",
Journal of Molecular Biology, vol. 325, pp. 555–567, 2003.
Onufriev, A., A. Smondyrev, and D. Bashford,
"Proton Affinity Changes Driving Uni- directional Proton Transport in the Bacteriorhodopsin Photocycle",
Journal of Molecular Biology , vol. 232, pp. 1183–1193, 2003.
2002
Onufriev, A., D. Bashford, and D. A. Case,
"The Generalized Born Approximation: The Importance of Being Perfect",
Journal of Computational Chemistry , vol. 23, 2002.
2001
Onufriev, A., D. A. Case, and G. M. Ullmann,
"A Novel View of pH Titration in Biomolecules.",
Biochemistry , vol. 40, 2001.
2000
Onufriev, A., D. A. Case, and D. Bashford,
"A Modification of the Generalized Born Model Suitable for Macromolecules",
Journal of Physical Chemistry B , vol. 104, 2000.
1999
Onufriev, A., and J. B. Marston,
"Enlarged Symmetry and Coherence in Arrays of Quan- tum Dots.",
Phys. Rev. B, vol. 59, 1999.
1996
Onufriev, A., and J. B. Marston,
"Memory Loss and Auger Processes in a Many-Body Theory of Charge Transfer",
Phys. Rev. B., vol. 53, 1996.
1993
Onufriev, A., and D. S. Chernavskii,
"ATP Synthesis By Free and Membrane-Bound H+-ATPase of the Chloroplasts in Conditions of a pH shift",
Biophysics, vol. 38, no. 1005, 1993.
Please see projects at: http://people.cs.vt.edu/~onufriev/research/
ACC Research Scholars Program
Granting Institution: The Atlantic Coast Conference
Amount: $2,000
Analytical Electrostatics: Methods and Biological Applications
Granting Institution: National Institutes of Health
Amount: $1,286,940
Computational Models for Gene Silencing: Elucidating A Pervasive Biological Defense
Granting Institution: National Science Foundation
Amount: $1,267,410
Contribution of Nonlinear effects into DNA structural transformations and Mechanical Properties
Granting Institution: Civilian Research and Development Foundation
Amount: $30,000
DNA-DNA Interaction with Atomic Detail
Granting Institution: National Institute of Health
Amount: $1,334,220
Novel tools to understand the role of ions in nucleic acid structure and function
Granting Institution: National Institutes of Health
Amount: $433, 580
The Role of Nonlinear Excitations and Electrostatics in DNA Structural Transformation
Granting Institution: US CRDF
Amount: