Biblio

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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.
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.
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.
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.
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.
Ruscio, J. Z., 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, , (in press ), 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
Onufriev, A., "Implicit Solvent Models inMolecular Dynamics Simulations", Annual Review of Computational Chemistry, 2008.
2007
Mongan, J., A. Svrcek-Seiler, and A. Onufriev, "Analysis of integral expressions for effective Born radii", J. Chem. Phys., vol. 127, 2007.
Fenley, A. T., J. C. Gordon, and A. Onufriev, "An Analytical Approach to Computing Biomolecular Electrostatic Potential", J. Chem. Phys, 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.
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.
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.
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.
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.
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.
Sigalov, G., P. Scheffel, and A. Onufriev, "Incorporating various dielectric environments into the generalized Born model", J. Chem. Phys., vol. 122, 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., 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.