Recognition of docking sites on a protein using [beta]-shape based on Voronoi diagram of atoms

@article{citeulike:1049127, abstract = {A protein consists of atoms. Given a protein, the automatic recognition of depressed regions on the surface of the protein, often called docking sites or pockets, is important for the analysis of interaction between a protein and a ligand and facilitates fast development of new drugs.Presented in this paper is a geometric approach for the detection of docking sites using [beta]-shape which is based on the Voronoi diagram for atoms in Euclidean distance metric. We first propose a geometric construct called a [beta]-shape which represents the proximity among atoms on the surface of a protein. Then, using the [beta]-shape, which takes the size differences among different atoms into account, we present an algorithm to extract the pockets for the possible docking site on the surface of a protein.}, author = {Kim, Deok-Soo and Cho, Cheol-Hyung and Kim, Donguk and Cho, Youngsong}, citeulike-article-id = {1049127}, doi = {10.1016/j.cad.2005.11.008}, journal = {Computer-Aided Design}, keywords = {algorithm, binding, geometric, identification, protein, site}, month = {May}, number = {5}, pages = {431--443}, posted-at = {2007-01-18 18:56:02}, priority = {2}, title = {Recognition of docking sites on a protein using [beta]-shape based on Voronoi diagram of atoms}, url = {http://dx.doi.org/10.1016/j.cad.2005.11.008}, volume = {38}, year = {2006} }

TY - JOUR ID - citeulike:1049127 L3 - citeulike-article-id:1049127 N2 - A protein consists of atoms. Given a protein, the automatic recognition of depressed regions on the surface of the protein, often called docking sites or pockets, is important for the analysis of interaction between a protein and a ligand and facilitates fast development of new drugs.Presented in this paper is a geometric approach for the detection of docking sites using [beta]-shape which is based on the Voronoi diagram for atoms in Euclidean distance metric. We first propose a geometric construct called a [beta]-shape which represents the proximity among atoms on the surface of a protein. Then, using the [beta]-shape, which takes the size differences among different atoms into account, we present an algorithm to extract the pockets for the possible docking site on the surface of a protein. IS - 5 JF - Computer-Aided Design EP - 443 TI - Recognition of docking sites on a protein using [beta]-shape based on Voronoi diagram of atoms VL - 38 SP - 431 KW - algorithm KW - binding KW - geometric KW - identification KW - protein KW - site AU - Kim, Deok-Soo AU - Cho, Cheol-Hyung AU - Kim, Donguk AU - Cho, Youngsong PY - 2006/05// UR - http://dx.doi.org/10.1016/j.cad.2005.11.008 ER -