The DOI matches its Crossref record; 36 of the 36 references it cites were found in a registry or an index.
Evaluation of comparative protein modeling by M ODELLER
Abstract
We evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and human eosinophil neurotoxin that were calculated by M ODELLER, a program for comparative protein modeling by satisfaction of spatial restraints. The models have good stereochemistry and are at least as similar to the crystallographic structures as the closest template structures. The largest errors occur in the regions that were not aligned correctly or where the template structures are not similar to the correct structure. These regions correspond predominantly to exposed loops, insertions of any length, and non‐conserved side chains. When a template structure with more than 40% sequence identity to the target protein is available, the model is likely to have about 90% of the mainchain atoms modeled with an rms deviation from the X‐ray structure of ≈ 1 Å, in large part because the templates are likely to be that similar to the X‐ray structure of the target. This rms deviation is comparable to the overall differences between refined NMR and X‐ray crystallography structures of the same protein. © 1995 Wiley‐Liss, Inc.
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CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
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PROCHECK: a program to check the stereochemical quality of protein structures
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Self-citationMOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
Kraulis, P. J. (1991) · Journal of Applied Crystallography · doi:10.1107/s0021889891004399 · Cited by 14,085
Comparative Protein Modelling by Satisfaction of Spatial Restraints
Šali, A., & Blundell, T. L. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1626 · Cited by 12,977
Self-citationNeedleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
Assessment of protein models with three-dimensional profiles
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Cited by
Comparative Protein Structure Modeling of Genes and Genomes
Martí-Renom, M. A., Stuart, A. C., Fiser, A., Sánchez, R., Melo, F., & Šali, A. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.291 · Cited by 3,169
Self-citationStructural basis of lenalidomide-induced CK1α degradation by the CRL4CRBN ubiquitin ligase
Petzold, G., Fischer, E. S., & Thomä, N. H. (2016) · Nature · doi:10.1038/nature16979 · Cited by 620
Proikas-Cezanne, T., Waddell, S., Gaugel, A., Frickey, T., Lupas, A., & Nordheim, A. (2004) · Oncogene · doi:10.1038/sj.onc.1208331 · Cited by 332
Pandini, A., Denison, M. S., Song, Y., Soshilov, A. A., & Bonati, L. (2007) · Biochemistry · doi:10.1021/bi061460t · Cited by 160
Romanowski, M. J., Soccio, R. E., Breslow, J. L., & Burley, S. K. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052140699 · Cited by 162
Metadata
- Authors
- Šali, A., Potterton, L., Yuan, F., van Vlijmen, H., & Karplus, M.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 1995-11
- Volume
- 23
- Issue
- 3
- Pages
- 318-326
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2066142272
- Cited by
- 1,085
- References
- 36
- FWCI
- 3.20
- Type
- journal article
- Language
- en
- Open access
- closed
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- Šali, A., Potterton, L., Yuan, F., van Vlijmen, H., & Karplus, M. (1995). Evaluation of comparative protein modeling by M ODELLER. Proteins: Structure, Function, and Bioinformatics. https://doi.org/10.1002/prot.340230306
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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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