Pdb-tools: A swiss army knife for molecular structures [version 1; referees: 2 approved]

João P.G.L.M. Rodrigues; João M.C. Teixeira; Mikaël Trellet; Alexandre M.J.J. Bonvin

doi:10.12688/f1000research.17456.1

Pdb-tools: A swiss army knife for molecular structures [version 1; referees: 2 approved]

João P.G.L.M. Rodrigues
, João M.C. Teixeira
, Mikaël Trellet
, Alexandre M.J.J. Bonvin

Stanford University

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

Abstract

The pdb-tools are a collection of Python scripts for working with molecular structure data in the Protein Data Bank (PDB) format. They allow users to edit, convert, and validate PDB files, from the command-line, in a simple but efficient manner. The pdb-tools are implemented in Python, without any external dependencies, and are freely available under the open-source Apache License at https://github.com/haddocking/pdb-tools/ and on PyPI.

Original language	English
Article number	1961
Journal	F1000Research
Volume	2018
Issue number	7
DOIs	https://doi.org/10.12688/f1000research.17456.1
Publication status	Published - 1 Jan 2018

Funding

Grant information: J.P.G.L.M.R acknowledges funding from a Niels Stensen Fellowship and NIH grant R35GM122543. M.T. and A.M.J.J.B were supported by the European H2020 e-Infrastructure grant BioExcel (grant no. 675728).

Keywords

Bioinformatics
Chemistry
Macromolecules
PDB
Protein structure
Python
Structural biology

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10.12688/f1000research.17456.1

48a04300-10ca-4111-834a-6ced7075132f_17456_-_joao_rodriguesFinal published version, 971 KB

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AU - Bonvin, Alexandre M.J.J.

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KW - Bioinformatics

KW - Chemistry

KW - Macromolecules

KW - PDB

KW - Protein structure

KW - Python

KW - Structural biology

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ER -

Pdb-tools: A swiss army knife for molecular structures [version 1; referees: 2 approved]

Abstract

Funding

Keywords

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