title: Prediction of novel and analogous folds using fragment assembly and fold recognition.
abstract: A number of new and newly improved methods for predicting protein structure developed by the Jones-University College London group were used to make predictions for the CASP6 experiment. Structures were predicted with a combination of fold recognition methods (mGenTHREADER, nFOLD, and THREADER) and a substantially enhanced version of FRAGFOLD, our fragment assembly method. Attempts at automatic domain parsing were made using DomPred and DomSSEA, which are based on a secondary structure parsing algorithm and additionally for DomPred, a simple local sequence alignment scoring function. Disorder prediction was carried out using a new SVM-based version of DISOPRED. Attempts were also made at domain docking and "microdomain" folding in order to build complete chain models for some targets.
authors.affiliation: Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom.|Department of Biochemistry and Molecular Biology, University College London, London, United Kingdom.
authors.forename: D T
authors.initials: DT
authors.lastname: Jones
authors.affiliation: Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom.
authors.forename: K
authors.initials: K
authors.lastname: Bryson
authors.affiliation: Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom.
authors.forename: A
authors.initials: A
authors.lastname: Coleman
authors.affiliation: Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom.
authors.forename: L J
authors.initials: LJ
authors.lastname: McGuffin
authors.affiliation: Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom.
authors.forename: M I
authors.initials: MI
authors.lastname: Sadowski
authors.affiliation: Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom.
authors.forename: J S
authors.initials: JS
authors.lastname: Sodhi
authors.affiliation: Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom.
authors.forename: J J
authors.initials: JJ
authors.lastname: Ward
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D003201:Computers; D030562:Databases, Protein; D019281:Dimerization; D006801:Humans; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D016415:Sequence Alignment; D012984:Software