FilterDCA: Interpretable supervised contact prediction using inter-domain coevolution.

Details

Serval ID
serval:BIB_E83F9F5B7B12
Type
Article: article from journal or magazin.
Collection
Publications
Title
FilterDCA: Interpretable supervised contact prediction using inter-domain coevolution.
Journal
PLoS computational biology
Author(s)
Muscat M., Croce G., Sarti E., Weigt M.
ISSN
1553-7358 (Electronic)
ISSN-L
1553-734X
Publication state
Published
Issued date
10/2020
Peer-reviewed
Oui
Volume
16
Number
10
Pages
e1007621
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: epublish
Abstract
Predicting three-dimensional protein structure and assembling protein complexes using sequence information belongs to the most prominent tasks in computational biology. Recently substantial progress has been obtained in the case of single proteins using a combination of unsupervised coevolutionary sequence analysis with structurally supervised deep learning. While reaching impressive accuracies in predicting residue-residue contacts, deep learning has a number of disadvantages. The need for large structural training sets limits the applicability to multi-protein complexes; and their deep architecture makes the interpretability of the convolutional neural networks intrinsically hard. Here we introduce FilterDCA, a simpler supervised predictor for inter-domain and inter-protein contacts. It is based on the fact that contact maps of proteins show typical contact patterns, which results from secondary structure and are reflected by patterns in coevolutionary analysis. We explicitly integrate averaged contacts patterns with coevolutionary scores derived by Direct Coupling Analysis, improving performance over standard coevolutionary analysis, while remaining fully transparent and interpretable. The FilterDCA code is available at http://gitlab.lcqb.upmc.fr/muscat/FilterDCA.
Keywords
Computational Biology/methods, Models, Molecular, Protein Conformation, Proteins/chemistry, Sequence Analysis, Protein/methods, Software, Supervised Machine Learning
Pubmed
Web of science
Open Access
Yes
Create date
21/09/2023 14:32
Last modification date
25/05/2024 7:14
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