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2008
Anandakrishnan R., Onufriev A., "Analysis of basic clustering algorithms for nu- merical estimation of statistical averages in biomolecules", J. Comp. Biol., vol. 15, pp. 165–18, 2008. Tagged BibTex xml
Ruscio J.Z., Kumar D., Shukla M., Prisant M.G., Murali T M., Onufriev A., Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin, , (in press ), 2008. Tagged BibTex xml
Onufriev A., "Implicit Solvent Models inMolecular Dynamics Simulations", Annual Review of Computational Chemistry, 2008. Tagged BibTex xml
2007
Fenley A.T., Gordon J.C., Onufriev A., "An Analytical Approach to Computing Biomolecular Electrostatic Potential", J. Chem. Phys, 2007. Tagged BibTex xml
Mongan J., Svrcek-Seiler A., Onufriev A., "Analysis of integral expressions for effective Born radii", J. Chem. Phys., vol. 127, 2007. Tagged BibTex xml
Mongan J., Simmerling C., McCammon J A., Case D A., Onufriev A., "Generalized Born Model with a Simple, Robust Molecular Volume Correction", J. Chem. Theory and Comput, vol. 3, pp. 156-169, 2007. Tagged BibTex xml
Saha N., Watson L T., Kafadar K., Ramakrishnan N., Onufriev A., Mane S P., Vasquez-Robinet C., "Validation and estimation of parameters for a general probabilistic model of the PCR process", J. Comp. Biol., vol. 14, pp. 102–117, 2007. Tagged BibTex xml
2006
Ruscio J Z., Onufriev A., "A computational study of nucleosomal DNA flexibility", Bio- phys J , vol. 91, pp. 4121-4132, 2006. Tagged BibTex xml
Saha N., Watson L T., Kafadar K., Onufriev A., Ramakrishnan N., Vasquez-Robinet C., Watkinson J., "A general probabilistic model of the PCR process", Appl. Math. Comput, vol. 182 , pp. 232–243, 2006. Tagged BibTex xml
2005
Onufriev A., Ullmann G M., "Decomposing Complex Ligand Binding into Simple Com- ponents: Connections between Microscopic and Macroscopic models.", J. Phys. Chem. , vol. 108, pp. 11157–11169, 2005. Tagged BibTex xml
Sigalov G., Scheffel P., Onufriev A., "Incorporating various dielectric environments into the generalized Born model", J. Chem. Phys., vol. 122, 2005. Tagged BibTex xml
Case D A., Darden T., Cheatham T., Gohlke H., Merz K., Onufriev A., Luo R., Woods R., "The Amber Bio-molecular Simulation Programs", Journal of Computational Chemistry , vol. 26, pp. 1668-1688, 2005. Tagged BibTex xml
2004
Feig M., Onufriev A., Lee M S., Im W., Case D A., Brooks. C L., "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. Tagged BibTex xml