Abstractions, algorithms and data structures for structural bioinformatics in PyCogent.

ABSTRACT: To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent - a popular feature-rich framework for sequence-based bioinformatics, but one which has lacked equally powerful tools for handling stuctural/coordinate-based data. Extensible Python modules have been developed, which provide object-oriented abstractions (based on a hierarchical representation of macromolecules), efficient data structures (e.g.kD-trees), fast implementations of common algorithms (e.g. surface-area calculations), read/write support for Protein Data Bank-related file formats and wrappers for external command-line applications (e.g. Stride). Integration of this code into PyCogent is symbiotic, allow

SUBMITTER: Cieslik M 

PROVIDER: S-EPMC3253748 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature