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Bioinformatics Vol. 19 no. 3 2003
Pages 429-430
© 2003 Oxford University Press

Applications Note

PDP: protein domain parser

Nickolai Alexandrov 1 and Ilya Shindyalov 2,*

1 Ceres Inc., 3007 Malibu Canyon Road, Malibu, CA 90265, USA
2 San Diego Supercomputer Center, University of California, San Diego, MC 0537, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA

Received on November 29, 2001 ; revised on September 27, 2002 ; accepted on October 6, 2002

Summary: We have developed a program for automatic identification of domains in protein three-dimensional structures. Performance of the program was assessed by three different benchmarks: (i) by comparison with the expert-curated SCOP database of structural domains; (ii) by comparison with a collection of manual domain assignments; and (iii) by comparison with a set of 55 proteins, frequently used as a benchmark for automatic domain assignment. In all these benchmarks PDP identified domains correctly in more than 80% of proteins.

Availability: http://123d.ncifcrf.gov/

Contact: nicka{at}ceres-inc.com shindyal{at}sdsc.edu

* To whom correspondence should be addressed.


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