PDP: protein domain parser

UNLABELLED 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/.

[1]  A M Lesk,et al.  Folding units in globular proteins. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[2]  C Sander,et al.  Mapping the Protein Universe , 1996, Science.

[3]  Robert D. Finn,et al.  The Pfam protein families database , 2004, Nucleic Acids Res..

[4]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[5]  G M Crippen,et al.  The tree structural organization of proteins. , 1978, Journal of molecular biology.

[6]  R Nussinov,et al.  Fast protein fold recognition via sequence to structure alignment and contact capacity potentials. , 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[7]  C. Sander,et al.  Parser for protein folding units , 1994, Proteins.

[8]  M. Billeter,et al.  MOLMOL: a program for display and analysis of macromolecular structures. , 1996, Journal of molecular graphics.

[9]  Alex Bateman,et al.  The InterPro database, an integrated documentation resource for protein families, domains and functional sites , 2001, Nucleic Acids Res..

[10]  Ioannis Xenarios,et al.  DIP: the Database of Interacting Proteins , 2000, Nucleic Acids Res..

[11]  T L Blundell,et al.  An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins , 1995, Protein science : a publication of the Protein Society.

[12]  Ying Xu,et al.  Protein domain decomposition using a graph-theoretic approach , 2000, Bioinform..

[13]  J M Thornton,et al.  Domain assignment for protein structures using a consensus approach: Characterization and analysis , 1998, Protein science : a publication of the Protein Society.

[14]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

[15]  M J Sternberg,et al.  Identification and analysis of domains in proteins. , 1995, Protein engineering.