Effective Born radii in the generalized Born approximation: The importance of being perfect. - Alexey Onufriev; David A. Case; Donald Bashford (J. Comput. Chem., 2002)

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. - Michael Feig; Alexey Onufriev; Michael S. Lee; Wonpil Im; David A. Case; Charles L. Brooks III (J. Comput. Chem., 2004)

The Amber biomolecular simulation programs. - David A. Case; Thomas E. Cheatham III; Tom Darden; Holger Gohlke; Ray Luo 001; Kenneth M. Merz Jr.; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J. Woods (J. Comput. Chem., 2005)

H++: a server for estimating pKas and adding missing hydrogens to macromolecules. - John C. Gordon; Jonathan B. Myers; Timothy Folta; Valia Shoja; Lenwood S. Heath; Alexey Onufriev (Nucleic Acids Res., 2005)

A general probabilistic model of the PCR process. - Nilanjan Saha; Layne T. Watson; Karen Kafadar; Alexey Onufriev; Naren Ramakrishnan; Cecilia Vasquez-Robinet; Jonathan I. Watkinson (Appl. Math. Comput., 2006)

Validation and Estimation of Parameters for a General Probabilistic Model of the PCR Process. - Nilanjan Saha; Layne T. Watson; Karen Kafadar; Naren Ramakrishnan; Alexey Onufriev; Shrinivasrao P. Mane; Cecilia Vasquez-Robinet (J. Comput. Biol., 2007)

Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules. - Ramu Anandakrishnan; Alexey Onufriev (J. Comput. Biol., 2008)

An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions. - Ramu Anandakrishnan; Alexey Onufriev (J. Comput. Chem., 2010)

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. - Ramu Anandakrishnan; Boris Aguilar; Alexey Onufriev (Nucleic Acids Res., 2012)

Multiscale Approximation with Graphical Processing Units for Multiplicative Speedup in Molecular Dynamics. - Ramu Anandakrishnan; Mayank Daga; Alexey Onufriev; Wu-chun Feng (BCB, 2016)

Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies. - Negin Forouzesh; Saeed Izadi; Alexey V. Onufriev (J. Chem. Inf. Model., 2017)

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. - Arne Elofsson; Berk Hess; Erik Lindahl; Alexey Onufriev; David van der Spoel; Anders Wallqvist (PLoS Comput. Biol., 2019)

Robustness of Multidimensional Optimization Outcomes: A General Approach and a Case Study. - Negin Forouzesh; Layne T. Watson; Alexey V. Onufriev (SpringSim, 2020)

AmberTools. - 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; et al. (J. Chem. Inf. Model., 2023)

Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent. - Negin Forouzesh; Fatemeh Ghafouri; Igor S. Tolokh; Alexey V. Onufriev (J. Chem. Inf. Model., 2024)