Leri: A web-server for identifying protein functional networks from evolutionary couplings
Information on the co-evolution of amino acid pairs in a protein can be used for endeavors such as protein engineering, mutation design, and structure prediction. Here we report a method that captures significant determinants of proteins using estimated co-evolution information to identify networks...
Main Authors: | , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Elsevier
2021-01-01
|
Series: | Computational and Structural Biotechnology Journal |
Subjects: | |
Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037021002300 |
id |
doaj-209267cafbb94ce3aa71b57f073879d3 |
---|---|
record_format |
Article |
spelling |
doaj-209267cafbb94ce3aa71b57f073879d32021-06-23T04:19:53ZengElsevierComputational and Structural Biotechnology Journal2001-03702021-01-011935563563Leri: A web-server for identifying protein functional networks from evolutionary couplingsNgaam J. Cheung0Arun T. John Peter1Benoit Kornmann2Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Leri Ltd, Oxford, UK; Corresponding author at: Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.Institute of Biochemistry, ETH Zürich, Zürich 8092, SwitzerlandDepartment of Biochemistry, University of Oxford, Oxford OX1 3QU, UKInformation on the co-evolution of amino acid pairs in a protein can be used for endeavors such as protein engineering, mutation design, and structure prediction. Here we report a method that captures significant determinants of proteins using estimated co-evolution information to identify networks of residues, termed ”residue communities”, relevant to protein function. On the benchmark dataset (67 proteins with both catalytic and allosteric residues), the Pearson’s correlation between the identified residues in the communities at functional sites is 0.53, and it is higher than 0.8 by taking account of conserved residues derived from the method. On the endoplasmic reticulum-mitochondria encounter structure complex, the results indicate three distinguishable residue communities that are relevant to functional roles in the protein family, suggesting that the residue communities could be general evolutionary signatures in proteins. Based on the method, we provide a webserver for the scientific community to explore the signatures in protein families, which establishes a powerful tool to analyze residue-level profiling for the discovery of functional sites and biological pathway identification. This web-server is freely available for non-commercial users at https://kornmann.bioch.ox.ac.uk/leri/services/ecs.html, neither login nor e-mail required.http://www.sciencedirect.com/science/article/pii/S2001037021002300Residue communityEvolutionary coupling analysisFunctional networkLeri |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ngaam J. Cheung Arun T. John Peter Benoit Kornmann |
spellingShingle |
Ngaam J. Cheung Arun T. John Peter Benoit Kornmann Leri: A web-server for identifying protein functional networks from evolutionary couplings Computational and Structural Biotechnology Journal Residue community Evolutionary coupling analysis Functional network Leri |
author_facet |
Ngaam J. Cheung Arun T. John Peter Benoit Kornmann |
author_sort |
Ngaam J. Cheung |
title |
Leri: A web-server for identifying protein functional networks from evolutionary couplings |
title_short |
Leri: A web-server for identifying protein functional networks from evolutionary couplings |
title_full |
Leri: A web-server for identifying protein functional networks from evolutionary couplings |
title_fullStr |
Leri: A web-server for identifying protein functional networks from evolutionary couplings |
title_full_unstemmed |
Leri: A web-server for identifying protein functional networks from evolutionary couplings |
title_sort |
leri: a web-server for identifying protein functional networks from evolutionary couplings |
publisher |
Elsevier |
series |
Computational and Structural Biotechnology Journal |
issn |
2001-0370 |
publishDate |
2021-01-01 |
description |
Information on the co-evolution of amino acid pairs in a protein can be used for endeavors such as protein engineering, mutation design, and structure prediction. Here we report a method that captures significant determinants of proteins using estimated co-evolution information to identify networks of residues, termed ”residue communities”, relevant to protein function. On the benchmark dataset (67 proteins with both catalytic and allosteric residues), the Pearson’s correlation between the identified residues in the communities at functional sites is 0.53, and it is higher than 0.8 by taking account of conserved residues derived from the method. On the endoplasmic reticulum-mitochondria encounter structure complex, the results indicate three distinguishable residue communities that are relevant to functional roles in the protein family, suggesting that the residue communities could be general evolutionary signatures in proteins. Based on the method, we provide a webserver for the scientific community to explore the signatures in protein families, which establishes a powerful tool to analyze residue-level profiling for the discovery of functional sites and biological pathway identification. This web-server is freely available for non-commercial users at https://kornmann.bioch.ox.ac.uk/leri/services/ecs.html, neither login nor e-mail required. |
topic |
Residue community Evolutionary coupling analysis Functional network Leri |
url |
http://www.sciencedirect.com/science/article/pii/S2001037021002300 |
work_keys_str_mv |
AT ngaamjcheung leriawebserverforidentifyingproteinfunctionalnetworksfromevolutionarycouplings AT aruntjohnpeter leriawebserverforidentifyingproteinfunctionalnetworksfromevolutionarycouplings AT benoitkornmann leriawebserverforidentifyingproteinfunctionalnetworksfromevolutionarycouplings |
_version_ |
1721362574239334400 |