The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM
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.
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
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A new approach to protein fold recognition
Jones, D. T., Taylort, W. R., & Thornton, J. M. (1992) · Nature · doi:10.1038/358086a0 · Cited by 1,221
Cited by
Comparative protein structure modeling using MODELLER
Webb, B., & Sali, A. (2016) · Current Protocols in Protein Science · doi:10.1002/cpps.20 · Cited by 730
“Three other programs that implement this method are 3D-JIGSAW (Bates et al., 2001), RosettaCM (Song et al., 2013), and SWISS-MODEL (Schwede et al., 2003).”
MethodStork, M., Bos, M. P., Jongerius, I., de Kok, N., Schilders, I., Weynants, V. E., Poolman, J. T., & Tommassen, J. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000969 · Cited by 141
Rinnerthaler, M., Jarolim, S., Heeren, G., Palle, E., Perju, S., Klinger, H., Bogengruber, E., Madeo, F., Braun, R. J., Breitenbach-Koller, L., et al. (2006) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2006.05.022 · Cited by 101
Sitarz, A. K., Mikkelsen, J. D., & Meyer, A. S. (2016) · Critical Reviews in Biotechnology · doi:10.3109/07388551.2014.949617 · Cited by 99
Vilella, F., Alves, R., Rodríguez‐Manzaneque, M. T., Bellí, G., Swaminathan, S., Sunnerhagen, P., & Herrero, E. (2004) · Comparative and Functional Genomics · doi:10.1002/cfg.406 · Cited by 54
Metadata
- Authors
- Bates, P. A., Kelley, L. A., MacCallum, R. M., & Sternberg, M. J. E.
- Venue
- Proteins: Structure, Function, and Genetics
- Publisher
- Wiley
- Published
- 2001
- Volume
- 45
- Issue
- S5
- Pages
- 39-46
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2149480059
- Cited by
- 567
- References
- 3
- FWCI
- 5.86
- Type
- journal article
- Language
- en
- Open access
- closed
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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