Alexey V. Onufriev

The Amber biomolecular simulation programs

David A. Case, Thomas E. Cheatham, Tom Darden et al. · Journal of Computational Chemistry · 2005 · 9.6K citations · Full text

Natural Sciences, Biophysics, Chemistry +17

Exploring protein native states and large‐scale conformational changes with a modified generalized born model

Alexey V. Onufriev, Donald Bashford, David A. Case · Proteins Structure Function and Bioinformatics · 2004 · 2.5K citations

Natural Sciences, Biochemistry, Biophysics +17

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

Ramu Anandakrishnan, Boris Aguilar, Alexey V. Onufriev · Nucleic Acids Research · 2012 · 1.9K citations · Full text

Natural Sciences, Biophysics, Chemistry +16

AmberTools

David A. Case, Hasan Metin Aktulga, Kellon Belfon et al. · Journal of Chemical Information and Modeling · 2023 · 1.9K citations · Full text

Natural Sciences, Bioinformatics, Biophysics +15

H++: a server for estimating pKas and adding missing hydrogens to macromolecules

John Gordon, Joseph B. Myers, T. Folta et al. · Nucleic Acids Research · 2005 · 1.8K citations · Full text

Life Sciences, Biochemistry, Biophysics +17