ArticleBMC bioinformatics2009
p3d--Python module for structural bioinformatics.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- FANTEN: a new web-based interface for the analysis of magnetic anisotropy-induced NMR data.Journal of biomolecular NMR · 2015Article
- MetalS(3), a database-mining tool for the identification of structurally similar metal sites.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2014Article
- MetalPDB: a database of metal sites in biological macromolecular structures.Nucleic acids research · 2013Article
- Identification of key residues for pH dependent activation of violaxanthin de-epoxidase from Arabidopsis thaliana.PloS one · 2012Article
- Evolutionary dynamics on protein bi-stability landscapes can potentially resolve adaptive conflicts.PLoS computational biology · 2012Article
- Abstractions, algorithms and data structures for structural bioinformatics in PyCogent.Journal of applied crystallography · 2011Article
- In Silico Design of Novel Anticoagulant Peptides targeting Blood Coagulation Factor VIIa.Sultan Qaboos University medical journal · 2011Article
- Mutation analysis of violaxanthin de-epoxidase identifies substrate-binding sites and residues involved in catalysis.The Journal of biological chemistry · 2010Article
- p3d--Python module for structural bioinformatics.BMC bioinformatics · 2009Article
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Authors and funding
2 authors.
Funding
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Abstract
backgroundHigh-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code.
resultsp3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures.
conclusionp3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.
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Registered trials
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