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ThermoMutDB: a thermodynamic database for missense mutations

Proteins are intricate, dynamic structures, and small changes in their amino acid sequences can lead to large effects on their folding, stability and dynamics. To facilitate the further development and evaluation of methods to predict these changes, we have developed ThermoMutDB, a manually curated...

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Autores principales: Xavier, Joicymara S, Nguyen, Thanh-Binh, Karmarkar, Malancha, Portelli, Stephanie, Rezende, Pâmela M, Velloso, João P L, Ascher, David B, Pires, Douglas E V
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778973/
https://www.ncbi.nlm.nih.gov/pubmed/33095862
http://dx.doi.org/10.1093/nar/gkaa925
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author Xavier, Joicymara S
Nguyen, Thanh-Binh
Karmarkar, Malancha
Portelli, Stephanie
Rezende, Pâmela M
Velloso, João P L
Ascher, David B
Pires, Douglas E V
author_facet Xavier, Joicymara S
Nguyen, Thanh-Binh
Karmarkar, Malancha
Portelli, Stephanie
Rezende, Pâmela M
Velloso, João P L
Ascher, David B
Pires, Douglas E V
author_sort Xavier, Joicymara S
collection PubMed
description Proteins are intricate, dynamic structures, and small changes in their amino acid sequences can lead to large effects on their folding, stability and dynamics. To facilitate the further development and evaluation of methods to predict these changes, we have developed ThermoMutDB, a manually curated database containing >14,669 experimental data of thermodynamic parameters for wild type and mutant proteins. This represents an increase of 83% in unique mutations over previous databases and includes thermodynamic information on 204 new proteins. During manual curation we have also corrected annotation errors in previously curated entries. Associated with each entry, we have included information on the unfolding Gibbs free energy and melting temperature change, and have associated entries with available experimental structural information. ThermoMutDB supports users to contribute to new data points and programmatic access to the database via a RESTful API. ThermoMutDB is freely available at: http://biosig.unimelb.edu.au/thermomutdb.
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spelling pubmed-77789732021-01-06 ThermoMutDB: a thermodynamic database for missense mutations Xavier, Joicymara S Nguyen, Thanh-Binh Karmarkar, Malancha Portelli, Stephanie Rezende, Pâmela M Velloso, João P L Ascher, David B Pires, Douglas E V Nucleic Acids Res Database Issue Proteins are intricate, dynamic structures, and small changes in their amino acid sequences can lead to large effects on their folding, stability and dynamics. To facilitate the further development and evaluation of methods to predict these changes, we have developed ThermoMutDB, a manually curated database containing >14,669 experimental data of thermodynamic parameters for wild type and mutant proteins. This represents an increase of 83% in unique mutations over previous databases and includes thermodynamic information on 204 new proteins. During manual curation we have also corrected annotation errors in previously curated entries. Associated with each entry, we have included information on the unfolding Gibbs free energy and melting temperature change, and have associated entries with available experimental structural information. ThermoMutDB supports users to contribute to new data points and programmatic access to the database via a RESTful API. ThermoMutDB is freely available at: http://biosig.unimelb.edu.au/thermomutdb. Oxford University Press 2020-10-23 /pmc/articles/PMC7778973/ /pubmed/33095862 http://dx.doi.org/10.1093/nar/gkaa925 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Xavier, Joicymara S
Nguyen, Thanh-Binh
Karmarkar, Malancha
Portelli, Stephanie
Rezende, Pâmela M
Velloso, João P L
Ascher, David B
Pires, Douglas E V
ThermoMutDB: a thermodynamic database for missense mutations
title ThermoMutDB: a thermodynamic database for missense mutations
title_full ThermoMutDB: a thermodynamic database for missense mutations
title_fullStr ThermoMutDB: a thermodynamic database for missense mutations
title_full_unstemmed ThermoMutDB: a thermodynamic database for missense mutations
title_short ThermoMutDB: a thermodynamic database for missense mutations
title_sort thermomutdb: a thermodynamic database for missense mutations
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778973/
https://www.ncbi.nlm.nih.gov/pubmed/33095862
http://dx.doi.org/10.1093/nar/gkaa925
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