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| - Searching for Patterns of Amino Acids in 3D Protein Structures
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| - This paper describes the program ASSAM, which has been developed to search for patterns of amino acidside-chains in the 3D structures in the Protein Data Bank. ASSAM represents an amino acid by a vectordrawn from the main chain towards the functional part of the amino acid and then computes a graphrepresentation of a protein in which the individual side-chain vectors are the nodes and the intervectordistances are the edges. The presence of a query pattern in a Protein Data Bank structure can then be searchedfor by means of a subgraph isomorphism algorithm. Recent enhancements to ASSAM allow searches toinclude the following: the main-chain structure in addition to the side-chains; the secondary structure andsolvent accessibility of side-chains; allowable distances from a known binding-site; disulfide bridges; andimproved generic and wild-card queries. The effectiveness of these approaches is demonstrated by extensivesearches of the Protein Data Bank for typical 3D query patterns.
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