Alexey Onufriev

Publication Activity (10 Years)

Years Active: 2002-2019
Publications (10 Years): 2

Top Topics

Signal Transduction

Biological Systems

Protein Folding

Simulation Data

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. PLoS Comput. Biol. 15 (1) (2019)
Ramu Anandakrishnan, Mayank Daga, Alexey Onufriev, Wu-chun Feng
Multiscale Approximation with Graphical Processing Units for Multiplicative Speedup in Molecular Dynamics. BCB (2016)
Ramu Anandakrishnan, Boris Aguilar, Alexey Onufriev
prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Ramu Anandakrishnan, Alexey Onufriev
approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions. J. Comput. Chem. 31 (4) (2010)
Ramu Anandakrishnan, Alexey Onufriev
Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules. J. Comput. Biol. 15 (2) (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. J. Comput. Biol. 14 (1) (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. Appl. Math. Comput. 182 (1) (2006)
John C. Gordon, Jonathan B. Myers, Timothy Folta, Valia Shoja, Lenwood S. Heath, Alexey Onufriev
s and adding missing hydrogens to macromolecules. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
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. J. Comput. Chem. 26 (16) (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. J. Comput. Chem. 25 (2) (2004)
Alexey Onufriev, David A. Case, Donald Bashford
Effective Born radii in the generalized Born approximation: The importance of being perfect. J. Comput. Chem. 23 (14) (2002)