p3d – Python module for structural bioinformatics

Background High-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...

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Vydané v:BMC bioinformatics Ročník 10; číslo 1; s. 258
Hlavní autori: Fufezan, Christian, Specht, Michael
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 21.08.2009
BioMed Central Ltd
BMC
Predmet:
Algorithms
Analysis
Applications software
Bioinformatics
Biomedical and Life Sciences
Computational biology
Computational Biology - methods
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Databases, Protein
Life Sciences
Microarrays
Programming Languages
Protein Conformation
Proteins
Proteins - chemistry
Software
Structure
Germany
Structural Bioinformatics
Plane Class
Query Function
Complex Query
Vector Operation
ISSN:1471-2105, 1471-2105
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Shrnutí:Background High-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. Results p3d 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. Conclusion p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.
Bibliografia:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-10-258