Prediction of novel and analogous folds using fragment assembly and fold recognition
- 26 September 2005
- journal article
- research article
- Published by Wiley in Proteins-Structure Function and Bioinformatics
- Vol. 61 (S7) , 143-151
- https://doi.org/10.1002/prot.20731
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. Proteins 2005;Suppl 7:143–151.Keywords
This publication has 21 references indexed in Scilit:
- Protein structure prediction servers at University College LondonNucleic Acids Research, 2005
- SCOP database in 2004: refinements integrate structure and sequence family dataNucleic Acids Research, 2004
- The Pfam protein families databaseNucleic Acids Research, 2004
- Rapid protein domain assignment from amino acid sequence using predicted secondary structureProtein Science, 2002
- Protein secondary structure prediction based on position-specific scoring matrices 1 1Edited by G. Von HeijneJournal of Molecular Biology, 1999
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functionsJournal of Molecular Biology, 1997
- Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifsProteins-Structure Function and Bioinformatics, 1997
- A new approach to protein fold recognitionNature, 1992
- Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical featuresBiopolymers, 1983