Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm. Export

@article{citeulike:1531835, abstract = {This article describes the PROSPECTOR\_3 threading algorithm, which combines various scoring functions designed to match structurally related target/template pairs. Each variant described was found to have a Z-score above which most identified templates have good structural (threading) alignments, Z(struct) (Z(good)). 'Easy' targets with accurate threading alignments are identified as single templates with Z > Z(good) or two templates, each with Z > Z(struct), having a good consensus structure in mutually aligned regions. 'Medium' targets have a pair of templates lacking a consensus structure, or a single template for which Z(struct) < Z < Z(good). PROSPECTOR\_3 was applied to a comprehensive Protein Data Bank (PDB) benchmark composed of 1491 single domain proteins, 41-200 residues long and no more than 30\% identical to any threading template. Of the proteins, 878 were found to be easy targets, with 761 having a root mean square deviation (RMSD) from native of less than 6.5 A. The average contact prediction accuracy was 46\%, and on average 17.6 residue continuous fragments were predicted with RMSD values of 2.0 A. There were 606 medium targets identified, 87\% (31\%) of which had good structural (threading) alignments. On average, 9.1 residue, continuous fragments with RMSD of 2.5 A were predicted. Combining easy and medium sets, 63\% (91\%) of the targets had good threading (structural) alignments compared to native; the average target/template sequence identity was 22\%. Only nine targets lacked matched templates. Moreover, PROSPECTOR\_3 consistently outperforms PSIBLAST. Similar results were predicted for open reading frames (ORFS) < or =200 residues in the M. genitalium, E. coli and S. cerevisiae genomes. Thus, progress has been made in identification of weakly homologous/analogous proteins, with very high alignment coverage, both in a comprehensive PDB benchmark as well as in genomes.}, address = {Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington St., Suite 300, Buffalo, NY 14203, USA. skolnick@buffalo.edu}, author = {Skolnick, J. and Kihara, D. and Zhang, Y.}, citeulike-article-id = {1531835}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/prot.20106}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15229883}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15229883}, day = {15}, doi = {10.1002/prot.20106}, issn = {1097-0134}, journal = {Proteins}, keywords = {threading}, month = {August}, number = {3}, pages = {502--518}, posted-at = {2008-01-12 19:59:20}, priority = {2}, title = {Development and large scale benchmark testing of the PROSPECTOR\_3 threading algorithm.}, url = {http://dx.doi.org/10.1002/prot.20106}, volume = {56}, year = {2004} }

TY - JOUR ID - citeulike:1531835 L3 - citeulike-article-id:1531835 N2 - This article describes the PROSPECTOR_3 threading algorithm, which combines various scoring functions designed to match structurally related target/template pairs. Each variant described was found to have a Z-score above which most identified templates have good structural (threading) alignments, Z(struct) (Z(good)). 'Easy' targets with accurate threading alignments are identified as single templates with Z > Z(good) or two templates, each with Z > Z(struct), having a good consensus structure in mutually aligned regions. 'Medium' targets have a pair of templates lacking a consensus structure, or a single template for which Z(struct) < Z < Z(good). PROSPECTOR_3 was applied to a comprehensive Protein Data Bank (PDB) benchmark composed of 1491 single domain proteins, 41-200 residues long and no more than 30% identical to any threading template. Of the proteins, 878 were found to be easy targets, with 761 having a root mean square deviation (RMSD) from native of less than 6.5 A. The average contact prediction accuracy was 46%, and on average 17.6 residue continuous fragments were predicted with RMSD values of 2.0 A. There were 606 medium targets identified, 87% (31%) of which had good structural (threading) alignments. On average, 9.1 residue, continuous fragments with RMSD of 2.5 A were predicted. Combining easy and medium sets, 63% (91%) of the targets had good threading (structural) alignments compared to native; the average target/template sequence identity was 22%. Only nine targets lacked matched templates. Moreover, PROSPECTOR_3 consistently outperforms PSIBLAST. Similar results were predicted for open reading frames (ORFS) < or =200 residues in the M. genitalium, E. coli and S. cerevisiae genomes. Thus, progress has been made in identification of weakly homologous/analogous proteins, with very high alignment coverage, both in a comprehensive PDB benchmark as well as in genomes. IS - 3 JF - Proteins SN - 1097-0134 AD - Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington St., Suite 300, Buffalo, NY 14203, USA. skolnick@buffalo.edu EP - 518 TI - Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm. VL - 56 SP - 502 KW - threading AU - Skolnick, J AU - Kihara, D AU - Zhang, Y PY - 2004/08/15/ UR - http://dx.doi.org/10.1002/prot.20106 ER -