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Protein Structure Similarity Clustering: Dynamic Treatment Of Pdb Structures Facilitates Clustering, Bradley D. Charette, Richard G. Macdonald, Stefan Wetzel, David B. Berkowitz, Herbert Waldmann

David Berkowitz Publications

Protein structure similarity clustering (PSSC) [1]– [3] is one of a number of potential guiding principles [4], [5] that have been introduced to focus combinatorial-library design/ protein targeting. PSSC clusters protein targets with similar ligand-binding cores in which little sequence or functional similarity is evident. Lead compounds for one member of the cluster then provide novel starting points in chemical space for ligand development for other members of the PSSC.

We describe herein a new clustering procedure that lends itself to ligand docking, molecular dynamics (MD), and the vector-alignment-search-tool (VAST) [6] algorithm. This MD-assisted approach offers an alternative to the …