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Bioinformatics. 2003 Feb 12;19(3):429-30.

PDP: protein domain parser.

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  • 1Ceres Inc, 3007 Malibu Canyon Road, Malibu, CA 90265, USA.


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.


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