Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm

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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, Zstruct (Zgood). ‘Easy’ targets with accurate threading alignments are identified as single templates with Z > Zgood or two templates, each with Z > Zstruct, 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 Zstruct < Z < Zgood. 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 Å. The average contact prediction accuracy was 46%, and on average 17.6 residue continuous fragments were predicted with RMSD values of 2.0 Å. 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 Å 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) ≤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. Proteins 2004;55:000–000.