Prediction of novel and analogous folds using fragment assembly and fold recognition.
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.
Jones
D T
DT
Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom.|Department of Biochemistry and Molecular Biology, University College London, London, United Kingdom.
Bryson
K
K
Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom.
Coleman
A
A
Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom.
McGuffin
L J
LJ
Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom.
Sadowski
M I
MI
Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom.
Sodhi
J S
JS
Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom.
Ward
J J
JJ
Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom.
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