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The protein common assembly database (ProtCAD)—a comprehensive structural resource of protein complexes
Proteins often act through oligomeric interactions with other proteins. X-ray crystallography and cryo-electron microscopy provide detailed information on the structures of biological assemblies, defined as the most likely biologically relevant structures derived from experimental data. In crystal s...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825537/ https://www.ncbi.nlm.nih.gov/pubmed/36300618 http://dx.doi.org/10.1093/nar/gkac937 |
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author | Xu, Qifang Dunbrack, Roland L |
author_facet | Xu, Qifang Dunbrack, Roland L |
author_sort | Xu, Qifang |
collection | PubMed |
description | Proteins often act through oligomeric interactions with other proteins. X-ray crystallography and cryo-electron microscopy provide detailed information on the structures of biological assemblies, defined as the most likely biologically relevant structures derived from experimental data. In crystal structures, the most relevant assembly may be ambiguously determined, since multiple assemblies observed in the crystal lattice may be plausible. It is estimated that 10–15% of PDB entries may have incorrect or ambiguous assembly annotations. Accurate assemblies are required for understanding functional data and training of deep learning methods for predicting assembly structures. As with any other kind of biological data, replication via multiple independent experiments provides important validation for the determination of biological assembly structures. Here we present the Protein Common Assembly Database (ProtCAD), which presents clusters of protein assembly structures observed in independent structure determinations of homologous proteins in the Protein Data Bank (PDB). ProtCAD is searchable by PDB entry, UniProt identifiers, or Pfam domain designations and provides downloads of coordinate files, PyMol scripts, and publicly available assembly annotations for each cluster of assemblies. About 60% of PDB entries contain assemblies in clusters of at least 2 independent experiments. All clusters and coordinates are available on ProtCAD web site (http://dunbrack2.fccc.edu/protcad). |
format | Online Article Text |
id | pubmed-9825537 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-98255372023-01-10 The protein common assembly database (ProtCAD)—a comprehensive structural resource of protein complexes Xu, Qifang Dunbrack, Roland L Nucleic Acids Res Database Issue Proteins often act through oligomeric interactions with other proteins. X-ray crystallography and cryo-electron microscopy provide detailed information on the structures of biological assemblies, defined as the most likely biologically relevant structures derived from experimental data. In crystal structures, the most relevant assembly may be ambiguously determined, since multiple assemblies observed in the crystal lattice may be plausible. It is estimated that 10–15% of PDB entries may have incorrect or ambiguous assembly annotations. Accurate assemblies are required for understanding functional data and training of deep learning methods for predicting assembly structures. As with any other kind of biological data, replication via multiple independent experiments provides important validation for the determination of biological assembly structures. Here we present the Protein Common Assembly Database (ProtCAD), which presents clusters of protein assembly structures observed in independent structure determinations of homologous proteins in the Protein Data Bank (PDB). ProtCAD is searchable by PDB entry, UniProt identifiers, or Pfam domain designations and provides downloads of coordinate files, PyMol scripts, and publicly available assembly annotations for each cluster of assemblies. About 60% of PDB entries contain assemblies in clusters of at least 2 independent experiments. All clusters and coordinates are available on ProtCAD web site (http://dunbrack2.fccc.edu/protcad). Oxford University Press 2022-10-27 /pmc/articles/PMC9825537/ /pubmed/36300618 http://dx.doi.org/10.1093/nar/gkac937 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://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 Xu, Qifang Dunbrack, Roland L The protein common assembly database (ProtCAD)—a comprehensive structural resource of protein complexes |
title | The protein common assembly database (ProtCAD)—a comprehensive structural resource of protein complexes |
title_full | The protein common assembly database (ProtCAD)—a comprehensive structural resource of protein complexes |
title_fullStr | The protein common assembly database (ProtCAD)—a comprehensive structural resource of protein complexes |
title_full_unstemmed | The protein common assembly database (ProtCAD)—a comprehensive structural resource of protein complexes |
title_short | The protein common assembly database (ProtCAD)—a comprehensive structural resource of protein complexes |
title_sort | protein common assembly database (protcad)—a comprehensive structural resource of protein complexes |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825537/ https://www.ncbi.nlm.nih.gov/pubmed/36300618 http://dx.doi.org/10.1093/nar/gkac937 |
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