PDP: protein domain parser | Zendy

Nickolai Alexandrov | Zendy; Ilya N. Shindyalov | Zendy

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PDP: protein domain parser

Author(s) -

Nickolai Alexandrov,

Ilya N. Shindyalov

Publication year - 2003

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btg006

Subject(s) - computer science , domain (mathematical analysis) , benchmark (surveying) , parsing , identification (biology) , set (abstract data type) , protein domain , programming language , data mining , biology , genetics , mathematical analysis , botany , mathematics , geodesy , gene , geography

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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