5714 Journal of Medicinal Chemistry, 2009, Vol. 52, No. 18 Irwin et al. Figure 3. Calibration docking report, containing pose fidelity (A˚ , rmsd) and enrichment (% rank) of the redocked crystallographic ligand compared to 100 property matched decoys using four para- metrizations, separated by a forward slash (/) in each cell. Successful runs are in green, unsuccessful ones in red, and marginal ones in yellow. Four parameter sets are evaluated by performing sam- pling and scoring each in two different ways. DOCK Blaster uses two different sampling schemes called “coarser” and “finer” to sample fewer or more ligand orientations by adjusting the bins used to generate initial orientations. The “coarser” scheme uses 45 “hot spots” and wider bins and generally runs somewhat faster, whereas “finer” uses 55 “hot spots”, narrower bins, and is often slower. Two scoring schemes called “polarized” and “normal” are also used. The “normal” scheme uses standard AMBER 94 partial atomic charges on the protein, while “polarized” increases the dipoles on selected polar atoms in residues within 3.5 A˚ of the crystallographic ligand without changing the net charge. In prospective studies involving experimental testing of novel inhibitors, we have found such limited polarization useful.41-44 Each ligand configuration that passes a rapid steric fit filter is scored for electrostatic and van der Waals complementarity and adjusted for partial ligand desolvation due to solvent occlusion.37 The high-scoring ligand confor- mation is minimized with 100 steps of simplex rigid-body minimization. More details of these schemes and other technical details may be found on the DOCK Blaster docu- mentation Web site, http://disi.docking.org/DOCK_Bla- ster:Technical_Details. d. The Calibrator. This subsystem evaluates how well docking works as judged by pose fidelity to the crystal structure and by enrichment versus decoys. In doing so, this tool selects the best docking parameters for a full database screen. It first redocks the ligand using all four docking parameter sets. It evaluates pose fidelity using the rmsd of all non-H atoms to the crystallographic pose and calculates the rank of the redocked ligand among the 100 property- matched decoys, which are also docked using all four dock- ing parameter sets. If actives and inactives were supplied, as is the case for the DUD benchmark, these are also docked and ROC plots are calculated. A concise calibration docking report allows users to judge which parametrization, if any, is best for prospective docking (Figure 3). Outcomes are color coded to indicate successful (in green), unsuccessful (in red), and borderline (in yellow) results. Particularly for borderline cases, the user may wish to inspect the scores and poses of each ligand and decoy before selecting the best parametrization for prospective docking. e. The Docker. This module screens (potentially very large) ZINC subsets on a computer cluster. It is normally only invoked after the calibrator has established that docking is viable. The most successful set of docking parameters from the calibration phase is selected and used. The Docker manages the screen across multiple CPUs, combining the results when the entire library has been searched. f. The Assessor. When database docking is complete, the Assessor prepares reports including full purchasing informa- tion, annotation of physical properties, annotation of known activities derived from public data sources, and similarity to annotated compounds, other top hits, and other purchasable compounds. Docked structures may be viewed in the context of the binding site using PyMol,45 Chimera46 or JMol.47 These reports may be browsed online or downloaded in tab-delim- ited format for processing by analysis software such as Excel. DOCK Blaster is accessible via a web-based interface at http://blaster.docking.org (Figure 1). It is hosted on a cluster of 700 CPU cores managed using the Sun Grid Engine with access to 30 terabytes of RAID-6 storage. DOCK Blaster is integrated with ZINC,39 a public access database of com- mercially available compounds for library screening, and the DUD Decoy Maker,27,40 which are also accessible sepa- rately. We do preserve the results of some screens, which we may use for methods development and analyses. DOCK Blaster was tested using ligand-bound crystal struc- tures from the PDB,48 including some of the most widely used benchmarking standards: Astex-85,7 GOLD-11415, and DUD-3827 (release 2, Oct 2006). We have used only the 38 structures in DUD for which a ligand-bound crystal structure is available. We have used only postremediation49 PDB structures for which a single small (<500 Da) organic ligand is bound, having 2.5 A˚ resolution or better, and no poly- nucleotides. Results DOCK Blaster is a new tool for automatic docking and is available for free anonymous public access at http://blaster. docking.org. DOCK Blaster can start from the structure of a target and a specification of the binding site or simply from a PDB code in many cases. To assess the performance of our automatic high throughput docking procedure retrospec- tively, we turned to common benchmarks in the field: Astex- 85,7 GOLD-114,15 and DUD-38.27 We began by retrieving the files directly from the remediated49 PDB and used the parser to automatically separate the ligand from the receptor. In all but a few cases, the parser succeeded well enough in this task to proceed to docking (Supporting Information Table S1). Occasionally the ligand could not be identified automatically. One reason was that the ligand was a common solute such as citrate. These could be rescued by simply specifying the three letter code of the ligand to the parser. The average total CPU time per target, from preparation to docking the ligand and its 100 decoys to final analysis of the results, all automated, was 92 min. Astex-85 Benchmarking. We began by using DOCK Blas- ter to automatically dock to targets in the Astex-85 set.7 In all but one case, the ligand was automatically separated from the protein starting from the PDB code alone (Supporting Information Table S1). For 1LF7, we were required to specify the ligand (citrate, CIT) because it is a common solute. Of the 84 jobs started automatically, 83 finished normally and produced a docked pose and score for the ligand and its decoys (Supporting Information Table S2). One ligand failed during conversion to SMILES (1U4D). We asked how well automatic docking could recapitulate the crystal structure using each of four docking parameter sets. Of the 83 protein-ligand pairs that yielded a docked ligand score, 51 were within 2 A˚ rmsd of the crystal structure