Facilities that make the PDB data collection more powerful

Joanna Lange, Coos Baakman, Arthur Pistorius, Elmar Krieger, Rob Hooft, Robbie P. Joosten, Gert Vriend

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

We describe a series of databases and tools that directly or indirectly support biomedical research on macromolecules, with focus on their applicability in protein structure bioinformatics research. DSSP, that determines secondary structures of proteins, has been updated to work well with extremely large structures in multiple formats. The PDBREPORT database that lists anomalies in protein structures has been remade to remove many small problems. These reports are now available as PDF-formatted files with a computer-readable summary. The VASE software has been added to analyze and visualize HSSP multiple sequence alignments for protein structures. The Lists collection of databases has been extended with a series of databases, most noticeably with a database that gives each protein structure a grade for usefulness in protein structure bioinformatics projects. The PDB-REDO collection of reanalyzed and re-refined protein structures that were solved by X-ray crystallography has been improved by dealing better with sugar residues and with hydrogen bonds, and adding many missing surface loops. All academic software underlying these protein structure bioinformatics applications and databases are now publicly accessible, either directly from the authors or from the GitHub software repository.

Original languageEnglish
Pages (from-to)330-344
Number of pages15
JournalProtein Science
Volume29
Issue number1
DOIs
Publication statusPublished - 1 Jan 2020

Fingerprint

Databases
Computational Biology
Proteins
Bioinformatics
Software
Secondary Protein Structure
Sequence Alignment
X Ray Crystallography
X ray crystallography
Macromolecules
Biomedical Research
Hydrogen
Sugars
Hydrogen bonds
Research

Keywords

  • bioinformatics support
  • DSSP
  • PDB
  • protein structure bioinformatics

Cite this

Lange, J., Baakman, C., Pistorius, A., Krieger, E., Hooft, R., Joosten, R. P., & Vriend, G. (2020). Facilities that make the PDB data collection more powerful. Protein Science, 29(1), 330-344. https://doi.org/10.1002/pro.3788
Lange, Joanna ; Baakman, Coos ; Pistorius, Arthur ; Krieger, Elmar ; Hooft, Rob ; Joosten, Robbie P. ; Vriend, Gert. / Facilities that make the PDB data collection more powerful. In: Protein Science. 2020 ; Vol. 29, No. 1. pp. 330-344.
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Lange, J, Baakman, C, Pistorius, A, Krieger, E, Hooft, R, Joosten, RP & Vriend, G 2020, 'Facilities that make the PDB data collection more powerful' Protein Science, vol. 29, no. 1, pp. 330-344. https://doi.org/10.1002/pro.3788

Facilities that make the PDB data collection more powerful. / Lange, Joanna; Baakman, Coos; Pistorius, Arthur; Krieger, Elmar; Hooft, Rob; Joosten, Robbie P.; Vriend, Gert.

In: Protein Science, Vol. 29, No. 1, 01.01.2020, p. 330-344.

Research output: Contribution to JournalArticleAcademicpeer-review

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Lange J, Baakman C, Pistorius A, Krieger E, Hooft R, Joosten RP et al. Facilities that make the PDB data collection more powerful. Protein Science. 2020 Jan 1;29(1):330-344. https://doi.org/10.1002/pro.3788