Structural Bioinformatics and Computational Molecular Biophysics
| Contact: Alexey Onufriev Our 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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We work at the interface of physics, biology, and computer science; the research is a collective effort of our group members who have background in one or more of these fields. The funding comes from the NIH and the NSF.
Active Research Areas:
- Biomolecular Electrostatics
- Protein Dynamics
- DNA compaction and bending; Modeling of nucleosome dynamics
- Insights into the RNAi mechanism
2015
Anandakrishnan, R., A. Drozdetski, R. C. Walker, and A. V. Onufriev,
"Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations",
Biophysical Journal, vol. 108, issue 5, pp. 1153 - 1164, 03/2015.
2014
Kinney, N. A., I. V. Sharakhov, and A. V. Onufriev,
"Investigation of the Chromosome Regions with Significant Affinity for the Nuclear Envelope in Fruit Fly – A Model Based Approach",
PLoS ONE, vol. 9, issue 3, pp. e91943, 3/2014.
Mukhopadhyay, A., B. H. Aguilar, I. S. Tolokh, and A. V. Onufriev,
"Introducing Charge Hydration Asymmetry into the Generalized Born Model",
Journal of Chemical Theory and Computation, 03/2014.
Onufriev, A. V., and B. Aguilar,
"Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions",
Journal of Theoretical and Computational Chemistry, pp. 140122232331001, 01/2014.
Tolokh, I. S., S. A. Pabit, A. M. Katz, Y. Chen, A. Drozdetski, N. Baker, L. Pollack, and A. V. Onufriev,
"Why double-stranded RNA resists condensation",
Nucleic Acids Research, vol. 42, issue 16, pp. 10823 - 10831, 09/2014.
Izadi, S., R. Anandakrishnan, and A. V. Onufriev,
"Building Water Models: A Different Approach",
The Journal of Physical Chemistry Letters, vol. 5, issue 21, pp. 3863 - 3871, 11/2014.
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.
Anandakrishnan, R., C. Baker, S. Izadi, and A. V. Onufriev,
"Point Charges Optimally Placed to Represent the Multipole Expansion of Charge Distributions",
PLoS ONE, vol. 8, issue 7, pp. e67715, 7/2013.
Onufriev, A. V., and E. Alexov,
"Protonation and pK changes in protein–ligand binding",
Quarterly Reviews of Biophysics, vol. 46, issue 02, pp. 181 - 209, 5/2013.
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.
Anandakrishnan, R.,
"A Partition Function Approximation Using Elementary Symmetric Functions",
PLOS one, vol. 7, no. 12, 12/2012.
Abstract
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.
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.
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.
Polys, N., Kim, S., and D. Bowman,
"Effects of Information Layout, Screen Size, and Field of View on User Performance in Information-Rich Virtual Environments",
Computer Animation and Virtual Worlds , vol. 18, no. 1, 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
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.
 | Alexey V OnufrievProfessor, Computer Science and Physics
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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
Novel tools to understand the role of ions in nucleic acid structure and function
Granting Institution: National Institutes of Health
Amount: $433, 580