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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-03-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/25/7/1522 |
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| author | Mikhail Yu. Lobanov Ilya V. Likhachev Oxana V. Galzitskaya |
| author_facet | Mikhail Yu. Lobanov Ilya V. Likhachev Oxana V. Galzitskaya |
| author_sort | Mikhail Yu. Lobanov |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-11T10:12:05Z |
| format | Article |
| id | doaj.art-b795b91c0a3a40ce824418098513a4ea |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-11T10:12:05Z |
| publishDate | 2020-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-b795b91c0a3a40ce824418098513a4ea2023-11-16T14:26:28ZengMDPI AGMolecules1420-30492020-03-01257152210.3390/molecules25071522Disordered Residues and Patterns in the Protein Data BankMikhail Yu. Lobanov0Ilya V. Likhachev1Oxana V. Galzitskaya2Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290 Moscow, RussiaInstitute of Protein Research, Russian Academy of Sciences, Pushchino, 142290 Moscow, RussiaInstitute of Protein Research, Russian Academy of Sciences, Pushchino, 142290 Moscow, RussiaWe 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.https://www.mdpi.com/1420-3049/25/7/1522disordered residuesidentityhomo-repeatsprotein structurelow complexity regions |
| spellingShingle | Mikhail Yu. Lobanov Ilya V. Likhachev Oxana V. Galzitskaya Disordered Residues and Patterns in the Protein Data Bank Molecules disordered residues identity homo-repeats protein structure low complexity regions |
| 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 | disordered residues identity homo-repeats protein structure low complexity regions |
| url | https://www.mdpi.com/1420-3049/25/7/1522 |
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