ProMod3-A versatile homology modelling toolbox.
Computational methods for protein structure modelling are routinely used to complement experimental structure determination, thus they help to address a broad spectrum of scientific questions in biomedical research. The most accurate methods today are based on homology modelling, i.e. detecting a ho...
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2021-01-01
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Series: | PLoS Computational Biology |
Online Access: | https://doi.org/10.1371/journal.pcbi.1008667 |
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doaj-10f104fd303b4f73b2d05258f3d116222021-05-19T04:31:37ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582021-01-01171e100866710.1371/journal.pcbi.1008667ProMod3-A versatile homology modelling toolbox.Gabriel StuderGerardo TaurielloStefan BienertMarco BiasiniNiklaus JohnerTorsten SchwedeComputational methods for protein structure modelling are routinely used to complement experimental structure determination, thus they help to address a broad spectrum of scientific questions in biomedical research. The most accurate methods today are based on homology modelling, i.e. detecting a homologue to the desired target sequence that can be used as a template for modelling. Here we present a versatile open source homology modelling toolbox as foundation for flexible and computationally efficient modelling workflows. ProMod3 is a fully scriptable software platform that can perform all steps required to generate a protein model by homology. Its modular design aims at fast prototyping of novel algorithms and implementing flexible modelling pipelines. Common modelling tasks, such as loop modelling, sidechain modelling or generating a full protein model by homology, are provided as production ready pipelines, forming the starting point for own developments and enhancements. ProMod3 is the central software component of the widely used SWISS-MODEL web-server.https://doi.org/10.1371/journal.pcbi.1008667 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Gabriel Studer Gerardo Tauriello Stefan Bienert Marco Biasini Niklaus Johner Torsten Schwede |
spellingShingle |
Gabriel Studer Gerardo Tauriello Stefan Bienert Marco Biasini Niklaus Johner Torsten Schwede ProMod3-A versatile homology modelling toolbox. PLoS Computational Biology |
author_facet |
Gabriel Studer Gerardo Tauriello Stefan Bienert Marco Biasini Niklaus Johner Torsten Schwede |
author_sort |
Gabriel Studer |
title |
ProMod3-A versatile homology modelling toolbox. |
title_short |
ProMod3-A versatile homology modelling toolbox. |
title_full |
ProMod3-A versatile homology modelling toolbox. |
title_fullStr |
ProMod3-A versatile homology modelling toolbox. |
title_full_unstemmed |
ProMod3-A versatile homology modelling toolbox. |
title_sort |
promod3-a versatile homology modelling toolbox. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Computational Biology |
issn |
1553-734X 1553-7358 |
publishDate |
2021-01-01 |
description |
Computational methods for protein structure modelling are routinely used to complement experimental structure determination, thus they help to address a broad spectrum of scientific questions in biomedical research. The most accurate methods today are based on homology modelling, i.e. detecting a homologue to the desired target sequence that can be used as a template for modelling. Here we present a versatile open source homology modelling toolbox as foundation for flexible and computationally efficient modelling workflows. ProMod3 is a fully scriptable software platform that can perform all steps required to generate a protein model by homology. Its modular design aims at fast prototyping of novel algorithms and implementing flexible modelling pipelines. Common modelling tasks, such as loop modelling, sidechain modelling or generating a full protein model by homology, are provided as production ready pipelines, forming the starting point for own developments and enhancements. ProMod3 is the central software component of the widely used SWISS-MODEL web-server. |
url |
https://doi.org/10.1371/journal.pcbi.1008667 |
work_keys_str_mv |
AT gabrielstuder promod3aversatilehomologymodellingtoolbox AT gerardotauriello promod3aversatilehomologymodellingtoolbox AT stefanbienert promod3aversatilehomologymodellingtoolbox AT marcobiasini promod3aversatilehomologymodellingtoolbox AT niklausjohner promod3aversatilehomologymodellingtoolbox AT torstenschwede promod3aversatilehomologymodellingtoolbox |
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1721437150212259840 |