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Bioinformatics Advance Access originally published online on August 29, 2006
Bioinformatics 2006 22(21):2695-2696; doi:10.1093/bioinformatics/btl461
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Barry J. Grant 1,*, Ana P. C. Rodrigues 2, Karim M. ElSawy 3, J. Andrew McCammon 1,4 and Leo S. D. Caves 3

1 Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
2 The Burnham Institute for Medical Research, La Jolla CA 92037, USA
3 Department of Biology, University of York York YO10 5YW, UK
4 Howard Hughes Medical Institute University of California, San Diego, La Jolla, CA 92093, USA

*To whom correspondence should be addressed.

Summary: 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/

Contact: bgrant{at}mccammon.ucsd.edu

Received on July 18, 2006; revised on August 22, 2006; accepted on August 23, 2006

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