MyPMFs: a simple tool for creating statistical potentials to assess protein structural models

Guillaume Postic; Thomas Wim Hamelryck; Jacques Chomilier; Dirk Stratmann

doi:10.1016/j.biochi.2018.05.013

MyPMFs: a simple tool for creating statistical potentials to assess protein structural models

Guillaume Postic, Thomas Wim Hamelryck, Jacques Chomilier, Dirk Stratmann

Computational and RNA Biology

3 Citations (Scopus)

Abstract

Evaluating the model quality of protein structures that evolve in environments with particular physicochemical properties requires scoring functions that are adapted to their specific residue compositions and/or structural characteristics. Thus, computational methods developed for structures from the cytosol cannot work properly on membrane or secreted proteins. Here, we present MyPMFs, an easy-to-use tool that allows users to train statistical potentials of mean force (PMFs) on the protein structures of their choice, with all parameters being adjustable. We demonstrate its use by creating an accurate statistical potential for transmembrane protein domains. We also show its usefulness to study the influence of the physical environment on residue interactions within protein structures. Our open-source software is freely available for download at https://github.com/bibip-impmc/mypmfs.

Original language	English
Journal	Biochimie
Volume	151
Pages (from-to)	37-41
Number of pages	5
ISSN	0300-9084
DOIs	https://doi.org/10.1016/j.biochi.2018.05.013
Publication status	Published - Aug 2018

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title = "MyPMFs: a simple tool for creating statistical potentials to assess protein structural models",

abstract = "Evaluating the model quality of protein structures that evolve in environments with particular physicochemical properties requires scoring functions that are adapted to their specific residue compositions and/or structural characteristics. Thus, computational methods developed for structures from the cytosol cannot work properly on membrane or secreted proteins. Here, we present MyPMFs, an easy-to-use tool that allows users to train statistical potentials of mean force (PMFs) on the protein structures of their choice, with all parameters being adjustable. We demonstrate its use by creating an accurate statistical potential for transmembrane protein domains. We also show its usefulness to study the influence of the physical environment on residue interactions within protein structures. Our open-source software is freely available for download at https://github.com/bibip-impmc/mypmfs.",

author = "Guillaume Postic and Hamelryck, {Thomas Wim} and Jacques Chomilier and Dirk Stratmann",

year = "2018",

month = aug,

doi = "10.1016/j.biochi.2018.05.013",

language = "English",

volume = "151",

pages = "37--41",

journal = "Biochimie",

issn = "0300-9084",

publisher = "Elsevier Masson",

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TY - JOUR

T1 - MyPMFs

T2 - a simple tool for creating statistical potentials to assess protein structural models

AU - Postic, Guillaume

AU - Hamelryck, Thomas Wim

AU - Chomilier, Jacques

AU - Stratmann, Dirk

PY - 2018/8

Y1 - 2018/8

N2 - Evaluating the model quality of protein structures that evolve in environments with particular physicochemical properties requires scoring functions that are adapted to their specific residue compositions and/or structural characteristics. Thus, computational methods developed for structures from the cytosol cannot work properly on membrane or secreted proteins. Here, we present MyPMFs, an easy-to-use tool that allows users to train statistical potentials of mean force (PMFs) on the protein structures of their choice, with all parameters being adjustable. We demonstrate its use by creating an accurate statistical potential for transmembrane protein domains. We also show its usefulness to study the influence of the physical environment on residue interactions within protein structures. Our open-source software is freely available for download at https://github.com/bibip-impmc/mypmfs.

AB - Evaluating the model quality of protein structures that evolve in environments with particular physicochemical properties requires scoring functions that are adapted to their specific residue compositions and/or structural characteristics. Thus, computational methods developed for structures from the cytosol cannot work properly on membrane or secreted proteins. Here, we present MyPMFs, an easy-to-use tool that allows users to train statistical potentials of mean force (PMFs) on the protein structures of their choice, with all parameters being adjustable. We demonstrate its use by creating an accurate statistical potential for transmembrane protein domains. We also show its usefulness to study the influence of the physical environment on residue interactions within protein structures. Our open-source software is freely available for download at https://github.com/bibip-impmc/mypmfs.

U2 - 10.1016/j.biochi.2018.05.013

DO - 10.1016/j.biochi.2018.05.013

M3 - Journal article

C2 - 29857183

SN - 0300-9084

VL - 151

SP - 37

EP - 41

JO - Biochimie

JF - Biochimie

ER -

MyPMFs: a simple tool for creating statistical potentials to assess protein structural models

Abstract

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