Protein Structure Similarity Clustering: Dynamic Treatment of PDB Structures Facilitates Clustering

Department of Chemistry, University of Nebraska at Lincoln, Lincoln, Nebraska, United States
Angewandte Chemie International Edition (Impact Factor: 11.26). 11/2006; 45(46):7766-70. DOI: 10.1002/anie.200602125
Source: PubMed

ABSTRACT In the family: The introduction of ligand docking, mol. dynamics, and the VAST algorithm into protein structure similarity clustering greatly streamlines the process and opens up otherwise unseen connections to new protein-cluster partners. VAST = vector alignment search tool. [on SciFinder(R)]

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Available from: David B Berkowitz, Sep 04, 2015
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    • "Protein sequence clustering methods can be classified according to two aspects: the clustering algorithm type used, which is usually either hierarchical or graph-based; and the criterion used to group sequences, which is usually either domain-based or family-based. On structural genomics studies, Charette et al. (2006) used protein clustering for protein ligand-docking and molecular dynamics, whereas Shen et al. (2005) used it for protein class prediction, and Yan and Moult (2005) searched for representative family structural templates. "
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