Bio3d: an R package for the comparative analysis of protein structures

Barry J Grant; Ana P C Rodrigues; Karim M ElSawy; J Andrew McCammon; Leo S D Caves

doi:10.1093/bioinformatics/btl461

Bio3d: an R package for the comparative analysis of protein structures

Bioinformatics. 2006 Nov 1;22(21):2695-6. doi: 10.1093/bioinformatics/btl461. Epub 2006 Aug 29.

Authors

Barry J Grant¹, Ana P C Rodrigues, Karim M ElSawy, J Andrew McCammon, Leo S D Caves

Affiliation

¹ Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA. bgrant@mccammon.ucsd.edu

PMID: 16940322
DOI: 10.1093/bioinformatics/btl461

Abstract

An automated procedure for the analysis of homologous protein structures has been developed. The method facilitates the characterization of internal conformational differences and inter-conformer relationships and provides a framework for the analysis of protein structural evolution. The method is implemented in bio3d, an R package for the exploratory analysis of structure and sequence data.

Availability: The bio3d package is distributed with full source code as a platform-independent R package under a GPL2 license from: http://mccammon.ucsd.edu/~bgrant/bio3d/

Publication types

Evaluation Study
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Amino Acid Sequence
Computer Simulation
Internet
Models, Chemical*
Models, Molecular*
Molecular Sequence Data
Protein Conformation
Proteins / chemistry*
Sequence Analysis, Protein / methods*
Software*
User-Computer Interface*

Substances

Proteins