The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Detection of common three‐dimensional substructures in proteins
Abstract
We present a fully automatic algorithm for three‐dimensional alignment of protein structures and for the detection of common substructures and structural repeats. Given two proteins, the algorithm first identifies all pairs of structurally similar fragments and subsequently clusters into larger units pairs of fragments that are compatible in three dimensions. The detection of similar substructures is independent of insertion/deletion penalties and can be chosen to be independent of the topology of loop connections and to allow for reversal of chain direction. Using distance geometry filters and other approximations, the algorithm, implemented in the WHAT IF program, is so fast that structural comparison of a single protein with the entire database of known protein structures can be performed routinely on a workstation. The method reproduces known non‐trivial superpositions such as plastocyanin on azurin. In addition, we report surprising structural similarity between ubiquitin and a (2Fe‐2S) ferredoxin.
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Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320
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Cited by
Combining evolutionary information and neural networks to predict protein secondary structure
Rost, B., & Sander, C. (1994) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340190108 · Cited by 1,452
Self-citationSurprising similarities in structure comparison
Gibrat, J.-F., Madej, T., & Bryant, S. H. (1996) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(96)80058-3 · Cited by 1,049
Selection of representative protein data sets
Hobohm, U., Scharf, M., Schneider, R., & Sander, C. (1992) · Protein Science · doi:10.1002/pro.5560010313 · Cited by 819
Self-citationBork, P., Sander, C., & Valencia, A. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.16.7290 · Cited by 811
Self-citationA New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology
Schmitt, S., Kuhn, D., & Klebe, G. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00811-2 · Cited by 423
Metadata
- Authors
- Vriend, G., & Sander, C.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 1991-09
- Volume
- 11
- Issue
- 1
- Pages
- 52-58
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2000468790
- Cited by
- 194
- References
- 1
- FWCI
- 5.07
- Type
- journal article
- Language
- en
- Open access
- closed
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- Vriend, G., & Sander, C. (1991). Detection of common three‐dimensional substructures in proteins. Proteins: Structure, Function, and Bioinformatics. https://doi.org/10.1002/prot.340110107
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