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Alexey Onufriev
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2020 – today
- 2023
- [j12]David A. Case
, Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros
, Vinícius Wilian D. Cruzeiro
, Negin Forouzesh, Timothy J. Giese
, Andreas W. Götz
, Holger Gohlke
, Saeed Izadi, Koushik Kasavajhala, Mehmet Cagri Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee
, Pengfei Li
, Jian Liu
, Tyler Luchko
, Ray Luo, Madushanka Manathunga
, Matías R. Machado
, Hai Minh Nguyen, Kurt A. O'Hearn, Alexey V. Onufriev
, Feng Pan
, Sergio Pantano
, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo
, Akhil Shajan, Jason M. Swails, Junmei Wang
, Haixin Wei
, Xiongwu Wu, Yongxian Wu
, Shi Zhang, Shiji Zhao
, Qiang Zhu
, Thomas E. Cheatham
, Daniel R. Roe, Adrian E. Roitberg
, Carlos Simmerling
, Darrin M. York
, Maria C. Nagan
, Kenneth M. Merz Jr.
:
AmberTools. J. Chem. Inf. Model. 63(20): 6183-6191 (2023) - 2020
- [c2]Negin Forouzesh, Layne T. Watson, Alexey V. Onufriev
:
Robustness of Multidimensional Optimization Outcomes: A General Approach and a Case Study. SpringSim 2020: 1-12
2010 – 2019
- 2019
- [j11]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) - 2017
- [j10]Negin Forouzesh
, Saeed Izadi, Alexey V. Onufriev
:
Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies. J. Chem. Inf. Model. 57(10): 2505-2513 (2017) - 2016
- [c1]Ramu Anandakrishnan
, Mayank Daga, Alexey Onufriev
, Wu-chun Feng:
Multiscale Approximation with Graphical Processing Units for Multiplicative Speedup in Molecular Dynamics. BCB 2016: 453-462 - 2012
- [j9]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 Res. 40(Web-Server-Issue): 537-541 (2012) - 2010
- [j8]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. J. Comput. Chem. 31(4): 691-706 (2010)
2000 – 2009
- 2008
- [j7]Ramu Anandakrishnan
, Alexey Onufriev
:
Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules. J. Comput. Biol. 15(2): 165-184 (2008) - 2007
- [j6]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): 97-112 (2007) - 2006
- [j5]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): 232-243 (2006) - 2005
- [j4]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): 1668-1688 (2005) - [j3]John C. Gordon, Jonathan B. Myers, Timothy Folta, Valia Shoja, Lenwood S. Heath, Alexey Onufriev
:
H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res. 33(Web-Server-Issue): 368-371 (2005) - 2004
- [j2]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): 265-284 (2004) - 2002
- [j1]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): 1297-1304 (2002)
Coauthor Index
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