Alexey Onufriev - researchr alias

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Viewing Publication 1 - 11 from 11

2019

Ten simple rules on how to create open access and reproducible molecular simulations of biological systemsArne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist. ploscb, 15(1), 2019. [doi]

2016

Multiscale Approximation with Graphical Processing Units for Multiplicative Speedup in Molecular DynamicsRamu Anandakrishnan, Mayank Daga, Alexey Onufriev, Wu-chun Feng. bcb 2016: 453-462 [doi]

2012

K prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulationsRamu Anandakrishnan, Boris Aguilar, Alexey Onufriev. nar, 40(Web-Server-Issue):537-541, 2012. [doi]

2010

An ::::N:::: log ::::N:::: approximation based on the natural organization of biomolecules for speeding up the computation of long range interactionsRamu Anandakrishnan, Alexey Onufriev. jcc, 31(4):691-706, 2010. [doi]

2008

Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in BiomoleculesRamu Anandakrishnan, Alexey Onufriev. jcb, 15(2):165-184, 2008. [doi]

2007

Validation and Estimation of Parameters for a General Probabilistic Model of the PCR ProcessNilanjan Saha, Layne T. Watson, Karen Kafadar, Naren Ramakrishnan, Alexey Onufriev, Shrinivasrao P. Mane, Cecilia Vasquez-Robinet. jcb, 14(1):97-112, 2007. [doi]

2006

A general probabilistic model of the PCR processNilanjan Saha, Layne T. Watson, Karen Kafadar, Alexey Onufriev, Naren Ramakrishnan, Cecilia Vasquez-Robinet, Jonathan I. Watkinson. amc, 182(1):232-243, 2006. [doi]

2005

The Amber biomolecular simulation programsDavid 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. jcc, 26(16):1668-1688, 2005. [doi]

H++: a server for estimating p::::K::::::a::s and adding missing hydrogens to macromoleculesJohn C. Gordon, Jonathan B. Myers, Timothy Folta, Valia Shoja, Lenwood S. Heath, Alexey Onufriev. nar, 33(Web-Server-Issue):368-371, 2005. [doi]

2004

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

2002

Effective Born radii in the generalized Born approximation: The importance of being perfectAlexey Onufriev, David A. Case, Donald Bashford. jcc, 23(14):1297-1304, 2002. [doi]

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