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Disordered Residues and Patterns in the Protein Data Bank
We created a new library of disordered patterns and disordered residues in the Protein Data Bank (PDB). To obtain such datasets, we clustered the PDB and obtained the groups of chains with different identities and marked disordered residues. We elaborated a new procedure for finding disordered patte...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7180803/ https://www.ncbi.nlm.nih.gov/pubmed/32230759 http://dx.doi.org/10.3390/molecules25071522 |
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author | Lobanov, Mikhail Yu. Likhachev, Ilya V. Galzitskaya, Oxana V. |
author_facet | Lobanov, Mikhail Yu. Likhachev, Ilya V. Galzitskaya, Oxana V. |
author_sort | Lobanov, Mikhail Yu. |
collection | PubMed |
description | We created a new library of disordered patterns and disordered residues in the Protein Data Bank (PDB). To obtain such datasets, we clustered the PDB and obtained the groups of chains with different identities and marked disordered residues. We elaborated a new procedure for finding disordered patterns and created a new version of the library. This library includes three sets of patterns: unique patterns, patterns consisting of two kinds of amino acids, and homo-repeats. Using this database, the user can: (1) find homologues in the entire Protein Data Bank; (2) perform a statistical analysis of disordered residues in protein structures; (3) search for disordered patterns and homo-repeats; (4) search for disordered regions in different chains of the same protein; (5) download clusters of protein chains with different identity from our database and library of disordered patterns; and (6) observe 3D structure interactively using MView. A new library of disordered patterns will help improve the accuracy of predictions for residues that will be structured or unstructured in a given region. |
format | Online Article Text |
id | pubmed-7180803 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-71808032020-05-01 Disordered Residues and Patterns in the Protein Data Bank Lobanov, Mikhail Yu. Likhachev, Ilya V. Galzitskaya, Oxana V. Molecules Article We created a new library of disordered patterns and disordered residues in the Protein Data Bank (PDB). To obtain such datasets, we clustered the PDB and obtained the groups of chains with different identities and marked disordered residues. We elaborated a new procedure for finding disordered patterns and created a new version of the library. This library includes three sets of patterns: unique patterns, patterns consisting of two kinds of amino acids, and homo-repeats. Using this database, the user can: (1) find homologues in the entire Protein Data Bank; (2) perform a statistical analysis of disordered residues in protein structures; (3) search for disordered patterns and homo-repeats; (4) search for disordered regions in different chains of the same protein; (5) download clusters of protein chains with different identity from our database and library of disordered patterns; and (6) observe 3D structure interactively using MView. A new library of disordered patterns will help improve the accuracy of predictions for residues that will be structured or unstructured in a given region. MDPI 2020-03-27 /pmc/articles/PMC7180803/ /pubmed/32230759 http://dx.doi.org/10.3390/molecules25071522 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Lobanov, Mikhail Yu. Likhachev, Ilya V. Galzitskaya, Oxana V. Disordered Residues and Patterns in the Protein Data Bank |
title | Disordered Residues and Patterns in the Protein Data Bank |
title_full | Disordered Residues and Patterns in the Protein Data Bank |
title_fullStr | Disordered Residues and Patterns in the Protein Data Bank |
title_full_unstemmed | Disordered Residues and Patterns in the Protein Data Bank |
title_short | Disordered Residues and Patterns in the Protein Data Bank |
title_sort | disordered residues and patterns in the protein data bank |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7180803/ https://www.ncbi.nlm.nih.gov/pubmed/32230759 http://dx.doi.org/10.3390/molecules25071522 |
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