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This study presents the (PS)<jats:sup>2<\/jats:sup>-v2 server, based on our original server with numerous enhancements and modifications, to improve reliability and applicability.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>To detect homologous proteins with remote similarity, the (PS)<jats:sup>2<\/jats:sup>-v2 server utilizes the S2A2 matrix, which is a 60 \u00d7 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)<jats:sup>2<\/jats:sup>-v2 is ranked 6<jats:sup>th<\/jats:sup> among 72 severs and is faster than the top-rank five serves, which utilize <jats:italic>ab initio<\/jats:italic> methods.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Experimental results demonstrate that (PS)<jats:sup>2<\/jats:sup>-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.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-10-366","type":"journal-article","created":{"date-parts":[[2009,10,31]],"date-time":"2009-10-31T19:20:43Z","timestamp":1257016843000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":96,"title":["(PS)2-v2: template-based protein structure prediction server"],"prefix":"10.1186","volume":"10","author":[{"given":"Chih-Chieh","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jenn-Kang","family":"Hwang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinn-Moon","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,10,31]]},"reference":[{"issue":"1","key":"3096_CR1","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1016\/j.sbi.2005.01.012","volume":"15","author":"P Aloy","year":"2005","unstructured":"Aloy P, Pichaud M, Russell RB: Protein complexes: structure prediction challenges for the 21(st) century. 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