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  Pmx: Automated protein structure and topology generation for alchemical perturbations.

Gapsys, V., Michielssens, S., Seeliger, D., & de Groot, B. L. (2015). Pmx: Automated protein structure and topology generation for alchemical perturbations. Journal of Computational Chemistry, 36(5), 348-354. doi:10.1002/jcc.23804.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0024-B8F6-6 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002A-0F42-F
Genre: Journal Article

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2087777.pdf (Publisher version), 491KB
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 Creators:
Gapsys, V.1, Author              
Michielssens, S.1, Author              
Seeliger, D.1, Author              
de Groot, B. L.1, Author              
Affiliations:
1Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578573              

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Free keywords: free energy calculations; molecular dynamics; alchemy; thermostability; mutations
 Abstract: Computational protein design requires methods to accurately estimate free energy changes in protein stability or binding upon an amino acid mutation. From the different approaches available, molecular dynamics-based alchemical free energy calculations are unique in their accuracy and solid theoretical basis. The challenge in using these methods lies in the need to generate hybrid structures and topologies representing two physical states of a system. A custom made hybrid topology may prove useful for a particular mutation of interest, however, a high throughput mutation analysis calls for a more general approach. In this work, we present an automated procedure to generate hybrid structures and topologies for the amino acid mutations in all commonly used force fields. The described software is compatible with the Gromacs simulation package. The mutation libraries are readily supported for five force fields, namely Amber99SB, Amber99SB*-ILDN, OPLS-AA/L, Charmm22*, and Charmm36.

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Language(s): eng - English
 Dates: 2014-12-082015-02-15
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1002/jcc.23804
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Title: Journal of Computational Chemistry
Source Genre: Journal
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Pages: - Volume / Issue: 36 (5) Sequence Number: - Start / End Page: 348 - 354 Identifier: -