Treffer: PyPDB: a Python API for the Protein Data Bank.

Title:
PyPDB: a Python API for the Protein Data Bank.
Authors:
Gilpin W; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2016 Jan 01; Vol. 32 (1), pp. 159-60. Date of Electronic Publication: 2015 Sep 14.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Databases, Protein* , Programming Languages* , Software* , User-Computer Interface*
Entry Date(s):
Date Created: 20150916 Date Completed: 20160801 Latest Revision: 20181202
Update Code:
20250114
DOI:
10.1093/bioinformatics/btv543
PMID:
26369703
Database:
MEDLINE

Weitere Informationen

Summary: We have created a Python programming interface for the RCSB Protein Data Bank (PDB) that allows search and data retrieval for a wide range of result types, including BLAST and sequence motif queries. The API relies on the existing XML-based API and operates by creating custom XML requests from native Python types, allowing extensibility and straightforward modification. The package has the ability to perform many types of advanced search of the PDB that are otherwise only available through the PDB website.
Availability and Implementation: PyPDB is implemented exclusively in Python 3 using standard libraries for maximal compatibility. The most up-to-date version, including iPython notebooks containing usage tutorials, is available free-of-charge under an open-source MIT license via GitHub at https://github.com/williamgilpin/pypdb, and the full API reference is at http://williamgilpin.github.io/pypdb_docs/html/. The latest stable release is also available on PyPI.
Contact: wgilpin@stanford.edu.
(© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)