SSThread : Template-free protein structure prediction by threading pairs of contacting secondary structures followed by assembly of overlapping pairs
Copyright © 2014 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 35(2014), 8 vom: 30. März, Seite 644-56 |
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| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2014
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article ab initio protein structure prediction contact map prediction knowledge-based potential loop closure secondary structure prediction Proteins Caspase 10 EC 3.4.22.- |
| Zusammenfassung: | Copyright © 2014 Wiley Periodicals, Inc. Acquiring the three-dimensional structure of a protein from its amino acid sequence alone, despite a great deal of work and significant progress on the subject, is still an unsolved problem. SSThread, a new template-free algorithm is described here that consists of making several predictions of contacting pairs of α-helices and β-strands derived from a database of experimental structures using a knowledge-based potential, secondary structure prediction, and contact map prediction followed by assembly of overlapping pair predictions to create an ensemble of core structure predictions whose loops are then predicted. In a set of seven CASP10 targets SSThread outperformed the two leading methods for two targets each. The targets were all β-strand containing structures and most of them have a high relative contact order which demonstrates the advantages of SSThread. The primary bottlenecks based on sets of 74 and 21 test cases are the pair prediction and loop prediction stages |
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| Beschreibung: | Date Completed 04.10.2014 Date Revised 18.02.2014 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.23543 |