PyPDB

PyPDB is a software tool for searching and retrieving data from the RCSB Protein Data Bank (PDB) using Python programming. It offers a wide range of search options, including BLAST and sequence motif queries, and can perform many types of advanced searches of the PDB that are otherwise only available through the PDB website. PyPDB provides an interface that creates custom XML requests from native Python types, making it highly extensible and easy to modify.

Moreover, PyPDB is implemented in Python 3, ensuring maximum compatibility with existing Python libraries. The latest version of the tool includes iPython notebooks containing usage tutorials, and the latest stable release of PyPDB is available on PyPI.

Topic

Molecular modelling;Sequence analysis;Proteins;Protein structure analysis

Detail

  • Operation: Protein structure analysis

  • Software interface: Command-line user interface

  • Language: Python

  • License: MIT License

  • Cost: Free

  • Version name: 2.2

  • Credit: -

  • Input: -

  • Output: -

  • Contact: William Gilpin wgilpin@stanford.edu

  • Collection: -

  • Maturity: Stable

Publications

Download and documentation

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