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Alexey V. Onufriev
Researcher at Virginia Tech
Publications - 118
Citations - 18851
Alexey V. Onufriev is an academic researcher from Virginia Tech. The author has contributed to research in topics: Solvation & Implicit solvation. The author has an hindex of 37, co-authored 102 publications receiving 15778 citations. Previous affiliations of Alexey V. Onufriev include Howard Hughes Medical Institute & Michigan State University.
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The Amber biomolecular simulation programs
David A. Case,Thomas E. Cheatham,Tom Darden,Holger Gohlke,Ray Luo,Kenneth M. Merz,Alexey V. Onufriev,Carlos Simmerling,Bing Wang,Robert J. Woods +9 more
TL;DR: The development, current features, and some directions for future development of the Amber package of computer programs, which contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
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Exploring protein native states and large-scale conformational changes with a modified generalized born model.
TL;DR: A popular analytical Generalized Born (GB) solvation model is modified to improve its accuracy in calculating the solvent polarization part of free energy changes in large‐scale conformational transitions, such as protein folding.
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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 V. Onufriev +5 more
TL;DR: The web server provides access to a tool that automates estimates of pKs as well as other related characteristics of biomolecules such as isoelectric points, titration curves and energies of protonation microstates, and is intended for a broad community of biochemists, molecular modelers, structural biologists and drug designers.
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H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
TL;DR: The latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.
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Modification of the Generalized Born Model Suitable for Macromolecules
TL;DR: The analytic generalized Born approximation is modified to permit a more accurate description of large macromolecules, while its established performance on small compounds is nearly unaffected, and is adapted to describe molecules with an interior dielectric constant not equal to unity.