Automatic atom type and bond type perception in molecular mechanical calculations.
By Junmei Wang, Wei Wang, Peter A. Kollman, David A. Case. Journal of Molecular Graphics and Modelling, 2006
5,066 citations recorded by the source corpus.
Subfields: Computational Theory and Mathematics, Materials Chemistry, Physical and Theoretical Chemistry
View Paper: https://www.semanticscholar.org/paper/2fcbf2c777b85ca0d77298c563b6ad78b1a52715
How researchers see this paper
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In Computational Theory and Mathematics
- Junmei Wang
- David L. Mobley
- J. Guthrie
- Wenbo Yu
- Alexander D. MacKerell
- Wim F. Vranken
- A. W. Sousa da Silva
- Dima Kozakov
In Materials Chemistry
- Junmei Wang
- T. Ferrin
- Thomas D. Goddard
- Wenbo Yu
- Eric F. Pettersen
- Alexander D. MacKerell
- Elaine C. Meng
- Vijay S. Pande
In Physical and Theoretical Chemistry
- Alexander D. MacKerell
- Wenbo Yu
- David L. Mobley
- Junmei Wang
- J. Guthrie
- Wim F. Vranken
- A. W. Sousa da Silva
- Vijay S. Pande
Citations in the corpus
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- Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies (2014, neutral): “Programs and web-servers that can be used to obtain parameters suitable for both atomistic simulations and computational drug design include: Antechamber which can provide parameters compatible with the Generalized Amber Force Feld (GAFF) [4, 5]; the YASARA AutoSMILES server [6] which also generates”
- Alchemical free energy methods for drug discovery: Progress and challenges (2011, background): “[67]), these often struggle with exotic chemistries, and there are numerous anecdotal reports of issues even for mundane chemistries.”
- A fast and high-quality charge model for the next generation general AMBER force field. (2020, methodology): “The Gaussian output files were directed to ANTECHAMBER 40 to generate the corresponding topology files (containing AM1-BCC atomic charges) and parameter files (including bonded terms and VDW terms) using the GAFF2 force field.”