An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins

R. Sowdhamini; Tom L. Blundell

doi:10.1002/pro.5560040317

journal article Open Access Mar 01, 1995

An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins

R. Sowdhamini Tom L. Blundell

Protein Science Vol. 4 No. 3 pp. 506-520 · Wiley

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Abstract

AbstractWith a growing number of structures available in the Brookhaven Protein Data Bank, automatic methods for domain identification are required for the construction of databases. Domains are considered to be clusters of secondary structure elements. Thus, helices and strands are first clustered using intersecondary structural distances between Cα positions, and dendrograms based on this distance measure are used to identify domains. Individual domains are recognized by a disjoint factor, which enables the automatic identification and classification into disjoint, interacting, and conjoint domains. Application to a database of 83 protein families and 18 unique structures shows that the approach provides an effective delineation of boundaries and identifies those proteins that can be considered as a single domain. A quantitative estimate of the interaction between domains has been proposed. The database of protein domains is a useful tool for understanding protein folding, for recognizing protein folds, and for understanding structure‐activity relationships.

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Metrics

67

Citations

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References

Details

Published: Mar 01, 1995
Vol/Issue: 4(3)
Pages: 506-520
License: View

Authors

University of Cambridge

Cite This Article

R. Sowdhamini, Tom L. Blundell (1995). An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. Protein Science, 4(3), 506-520. https://doi.org/10.1002/pro.5560040317

An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins

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