title: SSThread: Template-free protein structure prediction by threading pairs of contacting secondary structures followed by assembly of overlapping pairs.
abstract: 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.
authors: 15 Mitchell Ave, New Brunswick, NJ, 08901.
authors: Kevin J
authors: KJ
authors: Maurice
mesh_terms: D000465:Algorithms; D053455:Caspase 10 / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013379:Substrate Specificity
chemical_list: D011506:Proteins; D053455:Caspase 10
keywords: ab initio protein structure prediction; contact map prediction; knowledge-based potential; loop closure; secondary structure prediction