PDP: protein domain parser.
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.


BACKGROUND
http://123d.ncifcrf.gov/.
Alexandrov
Nickolai
N
Ceres Inc, 3007 Malibu Canyon Road, Malibu, CA 90265, USA. nicka@ceres-inc.com
Shindyalov
Ilya
I
D000465:Algorithms; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D011506:Proteins