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PDB-Tools Web: A user-friendly interface for the manipulation of PDB files
  • +2
  • Brian Jimenez-Garcia,
  • João Teixeira,
  • Mikael Trellet,
  • João Rodrigues,
  • Alexandre M.J.J. Bonvin
Brian Jimenez-Garcia
Utrecht University Faculty of Science
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João Teixeira
The Hospital for Sick Children
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Mikael Trellet
Utrecht University Faculty of Science
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João Rodrigues
Stanford University School of Medicine
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Alexandre M.J.J. Bonvin
Utrecht University Faculty of Science
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Abstract

The Protein Data Bank (PDB) file format remains a popular format used and supported by many software to represent coordinates of macromolecular structures. It however suffers from drawbacks such as error-prone manual editing. Because of that, various software toolkits have been developed to facilitate its editing and manipulation, but, to date, there is no online tool available for this purpose. Here we present PDB-Tools Web, a flexible online service for manipulating PDB files. It offers a rich and user-friendly graphical user interface that allows users to mix-and-match more than 40 individual tools from the pdb-tools suite. Those can be combined in a few clicks to perform complex pipelines, which can be saved and uploaded. The resulting processed PDB files can be visualized online and downloaded. The web server is freely available at https://wenmr.science.uu.nl/pdbtools.

Peer review status:UNDER REVIEW

03 Aug 2020Submitted to PROTEINS: Structure, Function, and Bioinformatics
05 Aug 2020Assigned to Editor
05 Aug 2020Submission Checks Completed
13 Sep 2020Reviewer(s) Assigned