Methodology article

(PS)²-v2: template-based protein structure prediction server

Chih-Chieh Chen¹ , Jenn-Kang Hwang^1,2,3 and Jinn-Moon Yang^1,2,3

¹  Institute of Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan, Republic of China

²  Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan, Republic of China

³  Molecular Bioinformatics Center, National Chiao Tung University, Hsinchu 30050, Taiwan, Republic of China

author email corresponding author email

BMC Bioinformatics 2009, 10:366doi:10.1186/1471-2105-10-366

Published:	31 October 2009

Abstract

Background

Template selection and target-template alignment are critical steps for template-based modeling (TBM) methods. To identify the template for the twilight zone of 15~25% sequence similarity between targets and templates is still difficulty for template-based protein structure prediction. This study presents the (PS)²-v2 server, based on our original server with numerous enhancements and modifications, to improve reliability and applicability.

Results

To detect homologous proteins with remote similarity, the (PS)²-v2 server utilizes the S2A2 matrix, which is a 60 × 60 substitution matrix using the secondary structure propensities of 20 amino acids, and the position-specific sequence profile (PSSM) generated by PSI-BLAST. In addition, our server uses multiple templates and multiple models to build and assess models. Our method was evaluated on the Lindahl benchmark for fold recognition and ProSup benchmark for sequence alignment. Evaluation results indicated that our method outperforms sequence-profile approaches, and had comparable performance to that of structure-based methods on these benchmarks. Finally, we tested our method using the 154 TBM targets of the CASP8 (Critical Assessment of Techniques for Protein Structure Prediction) dataset. Experimental results show that (PS)²-v2 is ranked 6^th among 72 severs and is faster than the top-rank five serves, which utilize ab initio methods.

Conclusion

Experimental results demonstrate that (PS)²-v2 with the S2A2 matrix is useful for template selections and target-template alignments by blending the amino acid and structural propensities. The multiple-template and multiple-model strategies are able to significantly improve the accuracies for target-template alignments in the twilight zone. We believe that this server is useful in structure prediction and modeling, especially in detecting homologous templates with sequence similarity in the twilight zone.