3DLigandSite: predicting ligand-binding sites using similar structures
نویسندگان
چکیده
3DLigandSite is a web server for the prediction of ligand-binding sites. It is based upon successful manual methods used in the eighth round of the Critical Assessment of techniques for protein Structure Prediction (CASP8). 3DLigandSite utilizes protein-structure prediction to provide structural models for proteins that have not been solved. Ligands bound to structures similar to the query are superimposed onto the model and used to predict the binding site. In benchmarking against the CASP8 targets 3DLigandSite obtains a Matthew's correlation co-efficient (MCC) of 0.64, and coverage and accuracy of 71 and 60%, respectively, similar results to our manual performance in CASP8. In further benchmarking using a large set of protein structures, 3DLigandSite obtains an MCC of 0.68. The web server enables users to submit either a query sequence or structure. Predictions are visually displayed via an interactive Jmol applet. 3DLigandSite is available for use at http://www.sbg.bio.ic.ac.uk/3dligandsite.
منابع مشابه
PoSSuM: a database of similar protein–ligand binding and putative pockets
Numerous potential ligand-binding sites are available today, along with hundreds of thousands of known binding sites observed in the PDB. Exhaustive similarity search for such vastly numerous binding site pairs is useful to predict protein functions and to enable rapid screening of target proteins for drug design. Existing databases of ligand-binding sites offer databases of limited scale. For ...
متن کاملInteraction of Human Serum Albumin with Ethyl 2-[2-(dimethylamino)-4-(4-nitrophenyl)-1,3-thiazole-5-yl]-2-oxoacetate as a Synthesized Ligand
The interaction of human serum albumin with Ethyl 2-[2-(dimethylamino)-4-(4-nitrophenyl)- 1,3-thiazole-5-yl]-2-oxoacetate was investigated by using isothermal titration UV-visible spectrophotometry in tris-buffer, pH 7.4. According to these results, it was found that there are a set of 4 binding sites for this ligand on HSA with positive cooperativity in the binding process. This thiazole deriv...
متن کاملPredicting small ligand binding sites in proteins using backbone structure
MOTIVATION Specific non-covalent binding of metal ions and ligands, such as nucleotides and cofactors, is essential for the function of many proteins. Computational methods are useful for predicting the location of such binding sites when experimental information is lacking. Methods that use structural information, when available, are particularly promising since they can potentially identify n...
متن کاملPredicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms
Predicting ligand binding sites (LBSs) on protein structures, which are obtained either from experimental or computational methods, is a useful first step in functional annotation or structure-based drug design for the protein structures. In this work, the structure-based machine learning algorithm ISMBLab-LIG was developed to predict LBSs on protein surfaces with input attributes derived from ...
متن کاملIn-silico Investigation of Tubulin Binding Modes of a Series of Novel Antiproliferative Spiroisoxazoline Compounds Using Docking Studies
Interference with microtubule polymerization results in cell cycle arrest leading to cell death. Colchicine is a well-known microtubule polymerization inhibitor which does so by binding to a specific site on tubulin. A set of 3',4'-bis (substituted phenyl)-4'H-spiro[indene-2,5'-isoxazol]-1(3H)-one derivatives with known antiproliferative activities were evaluated for their tubulin binding modes...
متن کامل