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  pmx Webserver: A user friendly interface for alchemistry

Gapsys, V., & de Groot, B. L. (2017). pmx Webserver: A user friendly interface for alchemistry. Journal of Chemical Information and Modeling, 57(2), 109-114. doi:10.1021/acs.jcim.6b00498.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002C-7A79-3 Version Permalink: http://hdl.handle.net/21.11116/0000-0001-21E1-B
Genre: Journal Article

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 Creators:
Gapsys, V.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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 Abstract: With the increase of available computational power and improvements in simulation algorithms, alchemical molecular dynamics based free energy calculations have developed into routine usage. To further facilitate the usability of alchemical methods for amino acid mutations, we have developed a web based infrastructure for obtaining hybrid protein structures and topologies. The presented webserver allows amino acid mutation selection in five contemporary molecular mechanics force fields. In addition, a complete mutation scan with a user defined amino acid is supported. The output generated by the webserver is directly compatible with the Gromacs molecular dynamics engine and can be used with any of the alchemical free energy calculation setup. Furthermore, we present a database of input files and precalculated free energy differences for tripeptides approximating a disordered state of a protein, of particular use for protein stability studies. Finally, the usage of the webserver and its output is exemplified by performing an alanine scan and investigating thermodynamic stability of the Trp cage mini protein. The webserver is accessible at http://pmx.mpibpc.mpg.de

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Language(s): eng - English
 Dates: 2017-02-092017-02-27
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1021/acs.jcim.6b00498
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Title: Journal of Chemical Information and Modeling
Source Genre: Journal
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Pages: - Volume / Issue: 57 (2) Sequence Number: - Start / End Page: 109 - 114 Identifier: -