Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: An automated all-against-all structural comparison using geometric matching Export

@article{citeulike:526143, abstract = {A method is described for the rapid comparison of protein binding sites using geometric matching to detect similar three-dimensional structure. The geometric matching detects common atomic features through identification of the maximum common sub-graph or clique. These features are not necessarily evident from sequence or from global structural similarity giving additional insight into molecular recognition not evident from current sequence or structural classification schemes. Here we use the method to produce an all-against-all comparison of phosphate binding sites in a number of different nucleotide phosphate-binding proteins. The similarity search is combined with clustering of similar sites to allow a preliminary structural classification. Clustering by site similarity produces a classification of binding sites for the 476 representative local environments producing ten main clusters representing half of the representative environments. The similarities make sense in terms of both structural and functional classification schemes. The ten main clusters represent a very limited number of unique structural binding motifs for phosphate. These are the structural P-loop, di-nucleotide binding motif [FAD/NAD(P)-binding and Rossman-like fold] and FAD-binding motif. Similar classification schemes for nucleotide binding proteins have also been arrived at independently by others using different methods. Proteins 2004. {\copyright} 2004 Wiley-Liss, Inc.}, address = {Department of Biochemistry \& Molecular Biology, University College London, Gower Street, London, England; School of Biochemistry \& Molecular Biology, University of Leeds, Leeds, England}, author = {Brakoulias, Andreas and Jackson, Richard M.}, citeulike-article-id = {526143}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/prot.20123}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15211509}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15211509}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/107643079/ABSTRACT}, day = {1}, doi = {10.1002/prot.20123}, issn = {1097-0134}, journal = {Proteins: Structure, Function, and Bioinformatics}, keywords = {bs-similarity, geometry-based, method, structure-classification}, month = {August}, number = {2}, pages = {250--260}, posted-at = {2006-03-02 02:30:36}, priority = {0}, title = {Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: An automated all-against-all structural comparison using geometric matching}, url = {http://dx.doi.org/10.1002/prot.20123}, volume = {56}, year = {2004} }

TY - JOUR ID - citeulike:526143 L3 - citeulike-article-id:526143 N2 - A method is described for the rapid comparison of protein binding sites using geometric matching to detect similar three-dimensional structure. The geometric matching detects common atomic features through identification of the maximum common sub-graph or clique. These features are not necessarily evident from sequence or from global structural similarity giving additional insight into molecular recognition not evident from current sequence or structural classification schemes. Here we use the method to produce an all-against-all comparison of phosphate binding sites in a number of different nucleotide phosphate-binding proteins. The similarity search is combined with clustering of similar sites to allow a preliminary structural classification. Clustering by site similarity produces a classification of binding sites for the 476 representative local environments producing ten main clusters representing half of the representative environments. The similarities make sense in terms of both structural and functional classification schemes. The ten main clusters represent a very limited number of unique structural binding motifs for phosphate. These are the structural P-loop, di-nucleotide binding motif [FAD/NAD(P)-binding and Rossman-like fold] and FAD-binding motif. Similar classification schemes for nucleotide binding proteins have also been arrived at independently by others using different methods. Proteins 2004. © 2004 Wiley-Liss, Inc. IS - 2 JF - Proteins: Structure, Function, and Bioinformatics SN - 1097-0134 AD - Department of Biochemistry & Molecular Biology, University College London, Gower Street, London, England; School of Biochemistry & Molecular Biology, University of Leeds, Leeds, England EP - 260 TI - Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: An automated all-against-all structural comparison using geometric matching VL - 56 SP - 250 KW - bs-similarity KW - geometry-based KW - method KW - structure-classification AU - Brakoulias, Andreas AU - Jackson, Richard PY - 2004/08/01/ UR - http://dx.doi.org/10.1002/prot.20123 ER -