Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM
- 1 January 2001
- journal article
- Published by Wiley in Proteins-Structure Function and Bioinformatics
- Vol. 45 (S5), 39-46
- https://doi.org/10.1002/prot.1168
Abstract
Fourteen models were constructed and analyzed for the comparative modeling section of Critical Assessment of Techniques for Protein Structure Prediction (CASP4). Sequence identity between each target and the best possible parent(s) ranged between 55 and 13%, and the root-mean-square deviation between model and target was from 0.8 to 17.9 A. In the fold recognition section, 10 of the 11 remote homologues were recognized. The modeling protocols are a combination of automated computer algorithms, 3D-JIGSAW (for comparative modeling) and 3D-PSSM (for fold recognition), with human intervention at certain critical stages. In particular, intervention is required to check superfamily assignment, best possible parents from which to model, sequence alignments to those parents and take-off regions for modeling variable regions. There now is a convergence of algorithms for comparative modeling and fold recognition, particularly in the region of remote homology.Keywords
This publication has 22 references indexed in Scilit:
- Enhanced genome annotation using structural profiles in the program 3D-PSSM 1 1Edited by J. ThorntonJournal of Molecular Biology, 2000
- Protein secondary structure prediction based on position-specific scoring matrices 1 1Edited by G. Von HeijneJournal of Molecular Biology, 1999
- Model building by comparison at CASP3: Using expert knowledge and computer automationProteins-Structure Function and Bioinformatics, 1999
- CASP3 comparative modeling evaluationProteins-Structure Function and Bioinformatics, 1999
- Structure classification-based assessment of CASP3 predictions for the fold recognition targetsProteins-Structure Function and Bioinformatics, 1999
- Large-scale protein structure modeling of the Saccharomyces cerevisiae genomeProceedings of the National Academy of Sciences, 1998
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- An automated classification of the structure of protein loopsJournal of Molecular Biology, 1997
- A strategy for the rapid multiple alignment of protein sequencesJournal of Molecular Biology, 1987
- Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical featuresBiopolymers, 1983