Cargando…
Twilight reloaded: the peptide experience
The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallographic studies of biomolecules with reasonably valid outcomes: that i...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2017
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5349433/ https://www.ncbi.nlm.nih.gov/pubmed/28291756 http://dx.doi.org/10.1107/S205979831601620X |
_version_ | 1782514466117648384 |
---|---|
author | Weichenberger, Christian X. Pozharski, Edwin Rupp, Bernhard |
author_facet | Weichenberger, Christian X. Pozharski, Edwin Rupp, Bernhard |
author_sort | Weichenberger, Christian X. |
collection | PubMed |
description | The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallographic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein–peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand. Here, the protein small-molecule ligand validation tool Twilight is updated to include peptide ligands. (i) The primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) a new method used to score peptide-ligand models is presented; (iii) a few instructive and specific examples, including an electron-density-based analysis of peptide-ligand structures that do not contain any ligands, are discussed in detail; (iv) means to avoid such mistakes and the implications for database integrity are discussed and (v) some suggestions as to how journal editors could help to expunge errors from the Protein Data Bank are provided. |
format | Online Article Text |
id | pubmed-5349433 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-53494332017-03-24 Twilight reloaded: the peptide experience Weichenberger, Christian X. Pozharski, Edwin Rupp, Bernhard Acta Crystallogr D Struct Biol Research Papers The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallographic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein–peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand. Here, the protein small-molecule ligand validation tool Twilight is updated to include peptide ligands. (i) The primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) a new method used to score peptide-ligand models is presented; (iii) a few instructive and specific examples, including an electron-density-based analysis of peptide-ligand structures that do not contain any ligands, are discussed in detail; (iv) means to avoid such mistakes and the implications for database integrity are discussed and (v) some suggestions as to how journal editors could help to expunge errors from the Protein Data Bank are provided. International Union of Crystallography 2017-02-28 /pmc/articles/PMC5349433/ /pubmed/28291756 http://dx.doi.org/10.1107/S205979831601620X Text en © Weichenberger et al. 2017 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 Weichenberger, Christian X. Pozharski, Edwin Rupp, Bernhard Twilight reloaded: the peptide experience |
title |
Twilight reloaded: the peptide experience |
title_full |
Twilight reloaded: the peptide experience |
title_fullStr |
Twilight reloaded: the peptide experience |
title_full_unstemmed |
Twilight reloaded: the peptide experience |
title_short |
Twilight reloaded: the peptide experience |
title_sort | twilight reloaded: the peptide experience |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5349433/ https://www.ncbi.nlm.nih.gov/pubmed/28291756 http://dx.doi.org/10.1107/S205979831601620X |
work_keys_str_mv | AT weichenbergerchristianx twilightreloadedthepeptideexperience AT pozharskiedwin twilightreloadedthepeptideexperience AT ruppbernhard twilightreloadedthepeptideexperience |