Improving threading algorithms for remote homology modeling by combining fragment and template comparisons

TitleImproving threading algorithms for remote homology modeling by combining fragment and template comparisons
Publication TypeJournal Article
Year of Publication2010
AuthorsZhou, H, Skolnick J
JournalProteins
Volume78
Pagination2041-8
Date Published2010 Jul
Abstract

In this work, we develop a method called fragment comparison and the template comparison (FTCOM) for assessing the global quality of protein structural models for targets of medium and hard difficulty (remote homology) produced by structure prediction approaches such as threading or ab initio structure prediction. FTCOM requires the C(alpha) coordinates of full length models and assesses model quality based on fragment comparison and a score derived from comparison of the model to top threading templates. On a set of 361 medium/hard targets, FTCOM was applied to and assessed for its ability to improve on the results from the SP(3), SPARKS, PROSPECTOR_3, and PRO-SP(3)-TASSER threading algorithms. The average TM-score improves by 5-10% for the first selected model by the new method over models obtained by the original selection procedure in the respective threading methods. Moreover, the number of foldable targets (TM-score >or= 0.4) increases from least 7.6% for SP(3) to 54% for SPARKS. Thus, FTCOM is a promising approach to template selection. Proteins 2010. (c) 2010 Wiley-Liss, Inc.

PDFhttp://cssb.biology.gatech.edu/skolnick/publications/pdffiles/310.pdf
Pub Med Link

http://www.ncbi.nlm.nih.gov/pubmed/20455261?dopt=Abstract

Alternate JournalProteins
Citekey310