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PDBFlex: exploring flexibility in protein structures
The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBF...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702920/ https://www.ncbi.nlm.nih.gov/pubmed/26615193 http://dx.doi.org/10.1093/nar/gkv1316 |
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author | Hrabe, Thomas Li, Zhanwen Sedova, Mayya Rotkiewicz, Piotr Jaroszewski, Lukasz Godzik, Adam |
author_facet | Hrabe, Thomas Li, Zhanwen Sedova, Mayya Rotkiewicz, Piotr Jaroszewski, Lukasz Godzik, Adam |
author_sort | Hrabe, Thomas |
collection | PubMed |
description | The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software. |
format | Online Article Text |
id | pubmed-4702920 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-47029202016-01-07 PDBFlex: exploring flexibility in protein structures Hrabe, Thomas Li, Zhanwen Sedova, Mayya Rotkiewicz, Piotr Jaroszewski, Lukasz Godzik, Adam Nucleic Acids Res Database Issue The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software. Oxford University Press 2016-01-04 2015-11-28 /pmc/articles/PMC4702920/ /pubmed/26615193 http://dx.doi.org/10.1093/nar/gkv1316 Text en © The Author(s) 2015. 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 Hrabe, Thomas Li, Zhanwen Sedova, Mayya Rotkiewicz, Piotr Jaroszewski, Lukasz Godzik, Adam PDBFlex: exploring flexibility in protein structures |
title | PDBFlex: exploring flexibility in protein structures |
title_full | PDBFlex: exploring flexibility in protein structures |
title_fullStr | PDBFlex: exploring flexibility in protein structures |
title_full_unstemmed | PDBFlex: exploring flexibility in protein structures |
title_short | PDBFlex: exploring flexibility in protein structures |
title_sort | pdbflex: exploring flexibility in protein structures |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702920/ https://www.ncbi.nlm.nih.gov/pubmed/26615193 http://dx.doi.org/10.1093/nar/gkv1316 |
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