| pubmed-article:7932758 | rdf:type | pubmed:Citation | lld:pubmed |
| pubmed-article:7932758 | lifeskim:mentions | umls-concept:C0020792 | lld:lifeskim |
| pubmed-article:7932758 | lifeskim:mentions | umls-concept:C0002520 | lld:lifeskim |
| pubmed-article:7932758 | lifeskim:mentions | umls-concept:C1510464 | lld:lifeskim |
| pubmed-article:7932758 | lifeskim:mentions | umls-concept:C0449774 | lld:lifeskim |
| pubmed-article:7932758 | lifeskim:mentions | umls-concept:C0449445 | lld:lifeskim |
| pubmed-article:7932758 | lifeskim:mentions | umls-concept:C0450363 | lld:lifeskim |
| pubmed-article:7932758 | pubmed:issue | 2 | lld:pubmed |
| pubmed-article:7932758 | pubmed:dateCreated | 1994-11-10 | lld:pubmed |
| pubmed-article:7932758 | pubmed:abstractText | This paper discusses the use of graph-theoretic methods for the representation and searching of three-dimensional patterns of side-chains in protein structures. The position of a side-chain is represented by pseudo-atoms, and the relative positions of pairs of side-chains by the distances between them. This description of the geometry can be represented by a labelled graph in which the nodes and the edges of the graph represent the pseudo-atoms and the sets of inter-pseudo-atomic distances, respectively. Given such a representation, a protein can be searched for the presence of a user-defined query pattern of side-chains by means of a subgraph-isomorphism algorithm which is implemented in the program ASSAM. Experiments with one such algorithm, that due to Ullmann, show that it provides both an effective and a highly efficient way of searching for patterns of side-chains. The method is illustrated by searches for the serine protease catalytic triad, for residues involved in the catalytic activity of staphyloccocal nuclease, and for the zinc-binding side-chains of thermolysin. The catalytic triad pattern search revealed the existence of a second Asp-His-Ser triad-like arrangement of residues in trypsinogen and chymotrypsinogen, in addition to the catalytic residues. In addition the program can be used to search for hypothetical patterns, as is shown for a pattern of three tryptophan side-chains. These searches demonstrate that the search algorithm can successfully retrieve the great majority of the expected proteins, as well as other, previously unreported proteins that contain the pattern of interest. | lld:pubmed |
| pubmed-article:7932758 | pubmed:language | eng | lld:pubmed |
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| pubmed-article:7932758 | pubmed:citationSubset | IM | lld:pubmed |
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| pubmed-article:7932758 | pubmed:status | MEDLINE | lld:pubmed |
| pubmed-article:7932758 | pubmed:month | Oct | lld:pubmed |
| pubmed-article:7932758 | pubmed:issn | 0022-2836 | lld:pubmed |
| pubmed-article:7932758 | pubmed:author | pubmed-author:RiceD WDW | lld:pubmed |
| pubmed-article:7932758 | pubmed:author | pubmed-author:ArtymiukP JPJ | lld:pubmed |
| pubmed-article:7932758 | pubmed:author | pubmed-author:WillettPP | lld:pubmed |
| pubmed-article:7932758 | pubmed:author | pubmed-author:PoirretteA... | lld:pubmed |
| pubmed-article:7932758 | pubmed:author | pubmed-author:GrindleyH MHM | lld:pubmed |
| pubmed-article:7932758 | pubmed:issnType | Print | lld:pubmed |
| pubmed-article:7932758 | pubmed:day | 21 | lld:pubmed |
| pubmed-article:7932758 | pubmed:volume | 243 | lld:pubmed |
| pubmed-article:7932758 | pubmed:owner | NLM | lld:pubmed |
| pubmed-article:7932758 | pubmed:authorsComplete | Y | lld:pubmed |
| pubmed-article:7932758 | pubmed:pagination | 327-44 | lld:pubmed |
| pubmed-article:7932758 | pubmed:dateRevised | 2006-11-15 | lld:pubmed |
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| pubmed-article:7932758 | pubmed:year | 1994 | lld:pubmed |
| pubmed-article:7932758 | pubmed:articleTitle | A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. | lld:pubmed |
| pubmed-article:7932758 | pubmed:affiliation | Krebs Institute for Biomolecular Research Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, U.K. | lld:pubmed |
| pubmed-article:7932758 | pubmed:publicationType | Journal Article | lld:pubmed |
| pubmed-article:7932758 | pubmed:publicationType | Research Support, Non-U.S. Gov't | lld:pubmed |
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