PDB-tools web: A user-friendly interface for the manipulation of PDB files

Brian Jiménez-García; João M C Teixeira; Mikael Trellet; João P G L M Rodrigues; Alexandre M J J Bonvin

doi:10.1002/prot.26018

PDB-tools web: A user-friendly interface for the manipulation of PDB files

Brian Jiménez-García, João M C Teixeira, Mikael Trellet, João P G L M Rodrigues, Alexandre M J J Bonvin

Research output: Contribution to journal › Article › Academic › peer-review

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.

Original language	English
Pages (from-to)	330-335
Number of pages	6
Journal	Proteins: Structure, Function and Genetics
Volume	89
Issue number	3
DOIs	https://doi.org/10.1002/prot.26018
Publication status	Published - Mar 2021

Keywords

PDB
bioinformatics
structural biology
web server

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10.1002/prot.26018

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title = "PDB-tools web: A user-friendly interface for the manipulation of PDB files",

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.",

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AU - Trellet, Mikael

AU - Rodrigues, João P G L M

AU - Bonvin, Alexandre M J J

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KW - structural biology

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PDB-tools web: A user-friendly interface for the manipulation of PDB files

Abstract

Keywords

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