Improving threading algorithms for remote homology modeling by combining fragment and template comparisons
- 18 March 2010
- journal article
- research article
- Published by Wiley in Proteins-Structure Function and Bioinformatics
- Vol. 78 (9), 2041-2048
- https://doi.org/10.1002/prot.22717
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.Keywords
Funding Information
- Division of General Medical Sciences of the National Institutes of Health (GM-48835, GM-37408)
This publication has 40 references indexed in Scilit:
- Protein Structure Prediction by Pro-Sp3-TASSERBiophysical Journal, 2009
- Performance of the Pro‐sp3‐TASSER server in CASP8Proteins-Structure Function and Bioinformatics, 2009
- Model quality assessment using distance constraints from alignmentsProteins-Structure Function and Bioinformatics, 2008
- Protein model quality assessment prediction by combining fragment comparisons and a consensus Cα contact potentialProteins-Structure Function and Bioinformatics, 2007
- QMEAN: A comprehensive scoring function for model quality assessmentProteins-Structure Function and Bioinformatics, 2007
- Ab Initio Protein Structure Prediction Using Chunk-TASSERBiophysical Journal, 2007
- A composite score for predicting errors in protein structure modelsProtein Science, 2006
- Single‐body residue‐level knowledge‐based energy score combined with sequence‐profile and secondary structure information for fold recognitionProteins-Structure Function and Bioinformatics, 2004
- GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequencesJournal of Molecular Biology, 1999
- Comparative Protein Modelling by Satisfaction of Spatial RestraintsJournal of Molecular Biology, 1993