title: Progress in fold recognition.
abstract: The prediction experiment reveals that fold recognition has become a powerful tool in structural biology. We applied our fold recognition technique to 13 target sequences. In two cases, replication terminating protein and prosequence of subtilisin, the predicted structures are very similar to the experimentally determined folds. For the first time, in a public blind test, the unknown structures of proteins have been predicted ahead of experiment to an accuracy approaching molecular detail. In two other cases the approximate folds have been predicted correctly. According to the assessors there were 12 recognizable folds among the target proteins. In our postprediction analysis we find that in 7 cases our fold recognition technique is successful. In several of the remaining cases the predicted folds have interesting features in common with the experimental results. We present our procedure, discuss the results, and comment on several fundamental and technical problems encountered in fold recognition.
authors.affiliation: Center for Applied Molecular Engineering, University of Salzburg, Austria.
authors.forename: H
authors.initials: H
authors.lastname: Flöckner
authors.forename: M
authors.initials: M
authors.lastname: Braxenthaler
authors.forename: P
authors.initials: P
authors.lastname: Lackner
authors.forename: M
authors.initials: M
authors.lastname: Jaritz
authors.forename: M
authors.initials: M
authors.lastname: Ortner
authors.forename: M J
authors.initials: MJ
authors.lastname: Sippl
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001426:Bacterial Proteins; D003195:Computer Communication Networks; D003196:Computer Graphics; D004268:DNA-Binding Proteins / Q000737:chemistry; D016208:Databases, Factual; D029721:Drosophila Proteins; D015801:Helminth Proteins; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000737:chemistry; D016415:Sequence Alignment; D012984:Software; D013381:Subtilisins / Q000737:chemistry; D014361:Trypsin Inhibitors / Q000737:chemistry; D043325:Xylan Endo-1,3-beta-Xylosidase; D014995:Xylosidases / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; C089851:C-E-1 inhibitor protein, Ascaris; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D015801:Helminth Proteins; D011506:Proteins; D016601:RNA-Binding Proteins; D014361:Trypsin Inhibitors; C063112:rtP protein, Bacillus subtilis; C069927:stau protein, Drosophila; D014995:Xylosidases; D043325:Xylan Endo-1,3-beta-Xylosidase; D013381:Subtilisins