Domain definition and target classification for CASP6

Assessment of structure predictions in CASP6 was based on single domains isolated from experimentally determined structures, which were categorized into comparative modeling, fold recognition, and new fold targets. Domain definitions were defined upon visual examination of the structures with the aid of automated domain‐parsing programs. Domain categorization was determined by comparison of the target structures with those in the Protein Data Bank at the time each target expired and a variety of sequence and structure‐based methods to determine potential homologous relationships. Proteins 2005;Suppl 7:8–18. © 2005 Wiley‐Liss, Inc.

[1]  N. Grishin,et al.  COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. , 2003, Journal of molecular biology.

[2]  Lisa N Kinch,et al.  CASP5 target classification , 2003, Proteins.

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

[4]  Ilya N. Shindyalov,et al.  PDP: protein domain parser , 2003, Bioinform..

[5]  John B. Anderson,et al.  CDD: a Conserved Domain Database for protein classification , 2004, Nucleic Acids Res..

[6]  Adam Zemla,et al.  LGA: a method for finding 3D similarities in protein structures , 2003, Nucleic Acids Res..

[7]  Woei-Jyh Lee,et al.  Evaluation of domain prediction in CASP6 , 2005, Proteins.

[8]  Jaswir Basran,et al.  Channelling and formation of ‘active’ formaldehyde in dimethylglycine oxidase , 2003, The EMBO journal.

[9]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[10]  R. Durbin,et al.  Pfam: A comprehensive database of protein domain families based on seed alignments , 1997, Proteins.

[11]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[12]  Osvaldo Olmea,et al.  MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison , 2002, Protein science : a publication of the Protein Society.

[13]  Roland L Dunbrack,et al.  Scoring profile‐to‐profile sequence alignments , 2004, Protein science : a publication of the Protein Society.

[14]  Dong Xu,et al.  Improving the performance of DomainParser for structural domain partition using neural network. , 2003, Nucleic acids research.

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