Alexey Onufriev

Ramu Anandakrishnan, Boris Aguilar, Alexey Onufriev: H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Research 40(Web-Server-Issue): 537-541 (2012)

Ramu Anandakrishnan, Alexey 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(4): 691-706 (2010)

Ramu Anandakrishnan, Alexey Onufriev: Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules. Journal of Computational Biology 15(2): 165-184 (2008)

Nilanjan Saha, Layne T. Watson, Karen Kafadar, Naren Ramakrishnan, Alexey Onufriev, Shrinivasrao P. Mane, Cecilia Vasquez-Robinet: Validation and Estimation of Parameters for a General Probabilistic Model of the PCR Process. Journal of Computational Biology 14(1): 97-112 (2007)

Nilanjan Saha, Layne T. Watson, Karen Kafadar, Alexey Onufriev, Naren Ramakrishnan, Cecilia Vasquez-Robinet, Jonathan I. Watkinson: A general probabilistic model of the PCR process. Applied Mathematics and Computation 182(1): 232-243 (2006)

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. Journal of Computational Chemistry 26(16): 1668-1688 (2005)

John C. Gordon, Jonathan B. Myers, Timothy Folta, Valia Shoja, Lenwood S. Heath, Alexey Onufriev: H++: a server for estimating pK_as and adding missing hydrogens to macromolecules. Nucleic Acids Research 33(Web-Server-Issue): 368-371 (2005)

Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks III: Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. Journal of Computational Chemistry 25(2): 265-284 (2004)

Alexey Onufriev, David A. Case, Donald Bashford: Effective Born radii in the generalized Born approximation: The importance of being perfect. Journal of Computational Chemistry 23(14): 1297-1304 (2002)