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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)
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