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Comparative Study
. 2003 Feb 12;19(3):429-30.
doi: 10.1093/bioinformatics/btg006.

PDP: protein domain parser

Nickolai Alexandrov  1 , Ilya Shindyalov
Affiliations
Comparative Study

PDP: protein domain parser

Nickolai Alexandrov et al. Bioinformatics. .

Abstract

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/.

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