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Homology-based loop modeling yields more complete crystallographic protein structures
Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completi...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6126648/ https://www.ncbi.nlm.nih.gov/pubmed/30224962 http://dx.doi.org/10.1107/S2052252518010552 |
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author | van Beusekom, Bart Joosten, Krista Hekkelman, Maarten L. Joosten, Robbie P. Perrakis, Anastassis |
author_facet | van Beusekom, Bart Joosten, Krista Hekkelman, Maarten L. Joosten, Robbie P. Perrakis, Anastassis |
author_sort | van Beusekom, Bart |
collection | PubMed |
description | Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completion of previously missing parts. This paper presents algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and ‘graft’ these regions of interest. These new regions are refined and validated in a fully automated procedure. Including these developments in the PDB-REDO pipeline has enabled the building of 24 962 missing loops in the PDB. The models and the automated procedures are publicly available through the PDB-REDO databank and webserver. More complete protein structure models enable a higher quality public archive but also a better understanding of protein function, better comparison between homologous structures and more complete data mining in structural bioinformatics projects. |
format | Online Article Text |
id | pubmed-6126648 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-61266482018-09-17 Homology-based loop modeling yields more complete crystallographic protein structures van Beusekom, Bart Joosten, Krista Hekkelman, Maarten L. Joosten, Robbie P. Perrakis, Anastassis IUCrJ Research Papers Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completion of previously missing parts. This paper presents algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and ‘graft’ these regions of interest. These new regions are refined and validated in a fully automated procedure. Including these developments in the PDB-REDO pipeline has enabled the building of 24 962 missing loops in the PDB. The models and the automated procedures are publicly available through the PDB-REDO databank and webserver. More complete protein structure models enable a higher quality public archive but also a better understanding of protein function, better comparison between homologous structures and more complete data mining in structural bioinformatics projects. International Union of Crystallography 2018-08-08 /pmc/articles/PMC6126648/ /pubmed/30224962 http://dx.doi.org/10.1107/S2052252518010552 Text en © van Beusekom et al. 2018 http://creativecommons.org/licenses/by/2.0/uk/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/2.0/uk/ |
spellingShingle | Research Papers van Beusekom, Bart Joosten, Krista Hekkelman, Maarten L. Joosten, Robbie P. Perrakis, Anastassis Homology-based loop modeling yields more complete crystallographic protein structures |
title | Homology-based loop modeling yields more complete crystallographic protein structures |
title_full | Homology-based loop modeling yields more complete crystallographic protein structures |
title_fullStr | Homology-based loop modeling yields more complete crystallographic protein structures |
title_full_unstemmed | Homology-based loop modeling yields more complete crystallographic protein structures |
title_short | Homology-based loop modeling yields more complete crystallographic protein structures |
title_sort | homology-based loop modeling yields more complete crystallographic protein structures |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6126648/ https://www.ncbi.nlm.nih.gov/pubmed/30224962 http://dx.doi.org/10.1107/S2052252518010552 |
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