title: Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing.
abstract: Analysis of the results of the recent protein structure prediction experiment for our method shows that we achieved a high level of success. Of the 18 available prediction targets of known structure, the assessors have identified 11 chains which either entirely match a previously known fold, or which partially match a substantial region of a known fold. Of these 11 chains, we made predictions for 9, and correctly assigned the folds in 5 cases. We have also identified a further 2 chains which also partially match known folds, and both of these were correctly predicted. The success rate for our method under blind testing is therefore 7 out of 11 chains. A further 2 folds could have easily been recognized but failed due to either overzealous filtering of potential matches, or to simple human error on our part. One of the two targets for which we did not submit a prediction, prosubtilisin, would not have been recognized by our usual criteria, but even in this case, it is possible that a correct prediction could have been made by considering a combination of pairwise energy and solvation energy Z-scores. Inspection of the threading alignments for the (alpha beta)8 barrels provides clues as to how fold recognition by threading works, in that these folds are recognized by parts rather than as a whole. The prospects for developing sequence threading technology further is discussed.
authors.affiliation: Department of Biochemistry and Molecular Biology, University College, London.
authors.forename: D T
authors.initials: DT
authors.lastname: Jones
authors.forename: R T
authors.initials: RT
authors.lastname: Miller
authors.forename: J M
authors.initials: JM
authors.lastname: Thornton
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001426:Bacterial Proteins; D002135:Calcium-Binding Proteins; D003195:Computer Communication Networks; D003196:Computer Graphics; D004268:DNA-Binding Proteins / Q000737:chemistry; D006026:Glycoside Hydrolases; D008562:Membrane Glycoproteins / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000737:chemistry; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D011772:Pyruvate, Orthophosphate Dikinase / Q000737:chemistry; D016415:Sequence Alignment; D012984:Software; D050857:Synaptotagmins; D013698:Templates, Genetic; D014510:Urease / Q000737:chemistry; D043325:Xylan Endo-1,3-beta-Xylosidase; D014995:Xylosidases / Q000737:chemistry; D001616:beta-Galactosidase / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D002135:Calcium-Binding Proteins; D004268:DNA-Binding Proteins; D008562:Membrane Glycoproteins; D009419:Nerve Tissue Proteins; D011506:Proteins; C063112:rtP protein, Bacillus subtilis; D050857:Synaptotagmins; D011772:Pyruvate, Orthophosphate Dikinase; D006026:Glycoside Hydrolases; D014995:Xylosidases; D001616:beta-Galactosidase; D043325:Xylan Endo-1,3-beta-Xylosidase; C022361:6-phospho-beta-galactosidase; D014510:Urease