title: SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles.
abstract: Structural flexibility of proteins has an important influence on molecular recognition and enzymatic function. In modeling, structure ensembles are therefore often applied as a valuable source of alternative protein conformations. However, their usage is often complicated by structural artifacts and inconsistent data annotation. Here, we present SIENA, a new computational approach for the automated assembly and preprocessing of protein binding site ensembles. Starting with an arbitrarily defined binding site in a single protein structure, SIENA searches for alternative conformations of the same or sequentially closely related binding sites. The method is based on an indexed database for identifying perfect k-mer matches and a recently published algorithm for the alignment of protein binding site conformations. Furthermore, SIENA provides a new algorithm for the interaction-based selection of binding site conformations which aims at covering all known ligand-binding geometries. Various experiments highlight that SIENA is able to generate comprehensive and well selected binding site ensembles improving the compatibility to both known and unconsidered ligand molecules. Starting with the whole PDB as data source, the computation time of the whole ensemble generation takes only a few seconds. SIENA is available via a Web service at www.zbh.uni-hamburg.de/siena .
authors.affiliation: Center for Bioinformatics, University of Hamburg , Bundesstrasse 43, 20146 Hamburg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Bietz
authors.affiliation: Center for Bioinformatics, University of Hamburg , Bundesstrasse 43, 20146 Hamburg, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Rarey
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D030562:Databases, Protein; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software; D013379:Substrate Specificity
chemical_list: D011506:Proteins