Abstract not found

In the past few years, pattern discovery has been emerging as a generic tool of choice for tackling problems from the computational biology domain. In this presentation, and after defining the problem in its generality, we review some of the algorithms that have appeared in the literature and describe several applications of pattern discovery to problems from computational biology. 2000 Academic Press 1.

Blind predictions of the local structure of nine CASP2 targets were made using the I-sites library of short sequence--- structure motifs, revealing strengths and weaknesses in this new knowledge-based method. Many turns between secondary structural elements were accurately predicted. Estimates of the confidence of prediction correlated well with the accuracy over the whole set. Bias toward structures used to develop the library was minimal, probably because of the extensive use of cross-validation. However, helix positions were better predicted by the PHD program. The method is likely to be sensitive to the quality of the sequence alignment. A general measure for evaluating local structure predictions is suggested. Proteins, Suppl. 1:167-- 171, 1997. r 1998 Wiley-Liss, Inc. Key words: sequence profiles building-blocks; secondary helix; strand turn knowledge-based

Rosettaabinitioproteinstructure predictionsinCASP4wereconsiderablymoreconsistentandmoreaccuratethanpreviousabinitio structurepredictions.Largesegmentswerecorrectlypredicted (>50residuessuperimposedwithin anRMSDof6.5)for16ofthe21domainsunder300 residuesforwhichmodelsweresubmitted.Models withtheglobalfoldlargelycorrectwereproduced forseveraltargetswithnewfolds,andforseveral difficultfoldrecognitiontargets,theRosettamodels weremoreaccuratethanthoseproducedwithtraditionalfoldrecognitionmodels. Thesepromising resultssuggestthatRosettamaysoonbeableto contributetotheinterpretationofgenomesequenceinformation. Proteins2001;Suppl5:119--126. 2002Wiley-Liss,Inc.

Local sequence-structure relationships in the loop regions of proteins were comprehensively estimated using simple prediction tools based on support vector regression (SVR). End-to-end distance was selected as a rough structural property of fragments, and the end-to-end distances of an enormous number of loop fragments from a wide variety of protein folds were directly predicted from sequence information by using SVR. We found that our method was more accurate than random prediction for predicting the structure of fragments comprising 5, 9, and 17 amino acids; moreover, the extended loop fragments could be successfully distinguished from turn structures on the basis of their sequences, which implies that the sequence-structure relationships were significant for loop fragments with a wide range of end-to-end distances. These results suggest that many loop regions as well as helices and strands restrict the conformational space of the entire tertiary structure of proteins to some extent; moreover, our findings throw light on the mechanism of protein folding and prediction of the tertiary structure of proteins without using structural templates.

ABSTRACT Rosetta ab initio protein structure predictions in CASP4 were considerably more consistent and more accurate than previous ab initio structure predictions. Large segments were correctly predicted (>50 residues superimposed within an RMSD of 6.5 Å) for 16 of the 21 domains under 300 residues for which models were submitted. Models with the global fold largely correct were produced for several targets with new folds, and for several difficult fold recognition targets, the Rosetta models were more accurate than those produced with traditional fold recognition models. These promising results suggest that Rosetta may soon be able to contribute to the interpretation of genome sequence information. Proteins 2001;Suppl 5:119–126. © 2002 Wiley-Liss, Inc.

ABSTRACT Rosettaabinitioproteinstructure predictions in CASP4 were considerably more consistent and more accurate than previous ab initio structure predictions. Large segments were correctlypredicted(>50residuessuperimposedwithin anRMSDof6.5Å)for16ofthe21domainsunder300 residues for which models were submitted. Models with the global fold largely correct were produced for several targets with new folds, and for several difficultfoldrecognitiontargets,theRosettamodels weremoreaccuratethanthoseproducedwithtraditional fold recognition models. These promising results suggest that Rosetta may soon be able to contribute to the interpretation of genome sequence information. Proteins 2001;Suppl 5:119–126. ©2002Wiley-Liss,Inc.

Motivation: The 3D structure of protein sequence A can be assembled by the substructures corresponding to small segments of A. A sequence segment does not take on all the structural fragments and thus it is desirable to build a short customized structural candidate list for each sequence segment. For each sequence segment, these substructures are its “specific structural alphabet”. The smaller these candidate lists are, the faster the protein structure can be constructed; the more accurate these candidate lists are, the more accurate the final protein structure will be. A major obstacle in protein structure prediction is to construct a small set of structural candidates for each segment such that the native structure can be rebuilt from these structural candidates accurately. Results: Based on integer linear programming and incorporating extra structural information, a software package FragShaver is developed.