{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,19]],"date-time":"2025-10-19T05:58:41Z","timestamp":1760853521525},"reference-count":23,"publisher":"Springer Science and Business Media LLC","issue":"S1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Native structures of proteins are formed essentially due to the combining effects of local and distant (in the sense of sequence) interactions among residues. These interaction information are, explicitly or implicitly, encoded into the scoring function in protein structure prediction approaches\u2014threading approaches usually measure an alignment in the sense that how well a sequence adopts an existing structure; while the energy functions in <jats:italic>Ab Initio<\/jats:italic> methods are designed to measure how likely a conformation is near-native. Encouraging progress has been observed in structure refinement where knowledge-based or physics-based potentials are designed to capture distant interactions. Thus, it is interesting to investigate whether distant interaction information captured by the <jats:italic>Ab Initio<\/jats:italic> energy function can be used to improve threading, especially for the weakly\/distant homologous templates.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In this paper, we investigate the possibility to improve alignment-generating through incorporating distant interaction information into the alignment scoring function in a nontrivial approach. Specifically, the distant interaction information is introduced through employing an <jats:italic>Ab Initio<\/jats:italic> energy function to evaluate the \u201cpartial\u201d decoy built from an alignment. Subsequently, a local search algorithm is utilized to optimize the scoring function.<\/jats:p>\n            <jats:p>Experimental results demonstrate that with distant interaction items, the quality of generated alignments are improved on 68 out of 127 query-template pairs in Prosup benchmark. In addition, compared with state-to-art threading methods, our method performs better on alignment accuracy comparison.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Incorporating <jats:italic>Ab Initio<\/jats:italic> energy functions into threading can greatly improve alignment accuracy.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-s1-s54","type":"journal-article","created":{"date-parts":[[2011,2,18]],"date-time":"2011-02-18T20:18:41Z","timestamp":1298060321000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Incorporating Ab Initio energy into threading approaches for protein structure prediction"],"prefix":"10.1186","volume":"12","author":[{"given":"Mingfu","family":"Shao","sequence":"first","affiliation":[]},{"given":"Sheng","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Chao","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Xiongying","family":"Yuan","sequence":"additional","affiliation":[]},{"given":"Shuai Cheng","family":"Li","sequence":"additional","affiliation":[]},{"given":"Weimou","family":"Zheng","sequence":"additional","affiliation":[]},{"given":"Dongbo","family":"Bu","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,2,15]]},"reference":[{"issue":"2","key":"4412_CR1","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1002\/prot.10521","volume":"54","author":"C Loose","year":"2004","unstructured":"Loose C, Klepeis J, Floudas C: A new pair-wise folding potential based on improved decoy generation and side-chain packing. 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