PDP: protein domain parser

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


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/.

Publication types

  • Comparative Study
  • Evaluation Study
  • Validation Study

MeSH terms

  • Algorithms*
  • Databases, Protein*
  • Information Storage and Retrieval / methods
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Tertiary*
  • Proteins / chemistry*
  • Sequence Analysis, Protein / methods*
  • Software


  • Proteins