Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. Export

@article{citeulike:977031, abstract = {Structure Based Drug Design (SBDD) is a computational approach to lead discovery that uses the three-dimensional structure of a protein to fit drug-like molecules into a ligand binding site to modulate function. Identifying the location of the binding site is therefore a vital first step in this process, restricting the search space for SBDD or virtual screening studies. The detection and characterisation of functional sites on proteins has increasingly become an area of interest. Structural genomics projects are increasingly yielding protein structures with unknown functions and binding sites. Binding site prediction was pioneered by pocket detection, since the binding site is often found in the largest pocket. More recent methods involve phylogenetic analysis, identifying structural similarity with proteins of known function and identifying regions on the protein surface with a potential for high binding affinity. Binding site prediction has been used in several SBDD projects and has been incorporated into several docking tools. We discuss different methods of ligand binding site prediction, their strengths and weaknesses, and how they have been used in SBDD.}, address = {Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.}, author = {Laurie, Alasdair T. and Jackson, Richard M.}, citeulike-article-id = {977031}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/17073692}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=17073692}, issn = {1389-2037}, journal = {Current protein \& peptide science}, keywords = {drug-design, minor-proposal}, month = {October}, number = {5}, pages = {395--406}, posted-at = {2006-12-06 19:26:00}, priority = {5}, title = {Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/17073692}, volume = {7}, year = {2006} }

TY - JOUR ID - citeulike:977031 L3 - citeulike-article-id:977031 N2 - Structure Based Drug Design (SBDD) is a computational approach to lead discovery that uses the three-dimensional structure of a protein to fit drug-like molecules into a ligand binding site to modulate function. Identifying the location of the binding site is therefore a vital first step in this process, restricting the search space for SBDD or virtual screening studies. The detection and characterisation of functional sites on proteins has increasingly become an area of interest. Structural genomics projects are increasingly yielding protein structures with unknown functions and binding sites. Binding site prediction was pioneered by pocket detection, since the binding site is often found in the largest pocket. More recent methods involve phylogenetic analysis, identifying structural similarity with proteins of known function and identifying regions on the protein surface with a potential for high binding affinity. Binding site prediction has been used in several SBDD projects and has been incorporated into several docking tools. We discuss different methods of ligand binding site prediction, their strengths and weaknesses, and how they have been used in SBDD. IS - 5 JF - Current protein & peptide science SN - 1389-2037 AD - Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK. EP - 406 TI - Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. VL - 7 SP - 395 KW - drug-design KW - minor-proposal AU - Laurie, Alasdair AU - Jackson, Richard PY - 2006/10// UR - http://view.ncbi.nlm.nih.gov/pubmed/17073692 ER -