title: CRDOCK: an ultrafast multipurpose protein-ligand docking tool.
abstract: An ultrafast docking and virtual screening program, CRDOCK, is presented that contains (1) a search engine that can use a variety of sampling methods and an initial energy evaluation function, (2) several energy minimization algorithms for fine tuning the binding poses, and (3) different scoring functions. This modularity ensures the easy configuration of custom-made protocols that can be optimized depending on the problem in hand. CRDOCK employs a precomputed library of ligand conformations that are initially generated from one-dimensional SMILES strings. Testing CRDOCK on two widely used benchmarks, the ASTEX diverse set and the Directory of Useful Decoys, yielded a success rate of ~75% in pose prediction and an average AUC of 0.66. A typical ligand can be docked, on average, in just ~13 s. Extension to a representative group of pharmacologically relevant G protein-coupled receptors that have been recently cocrystallized with some selective ligands allowed us to demonstrate the utility of this tool and also highlight some current limitations. CRDOCK is now included within VSDMIP, our integrated platform for drug discovery.
authors: Departamento de Farmacología, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain.
authors: Álvaro
authors: Á
authors: Cortés Cabrera
authors: Javier
authors: J
authors: Klett
authors: Helena G
authors: HG
authors: Dos Santos
authors: Almudena
authors: A
authors: Perona
authors: Rubén
authors: R
authors: Gil-Redondo
authors: Sandrea M
authors: SM
authors: Francis
authors: Eva M
authors: EM
authors: Priego
authors: Federico
authors: F
authors: Gago
authors: Antonio
authors: A
authors: Morreale
mesh_terms: D004353:Drug Evaluation, Preclinical / Q000379:methods*; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry / Q000378:metabolism; D013816:Thermodynamics; D013997:Time Factors; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D011506:Proteins; D043562:Receptors, G-Protein-Coupled