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...eduling. The MapReduce model has been applied to life science applications by many researchers. Qiu et al. [15] describe their work to implement various clustering algorithm using MapReduce. AutoDock =-=[13]-=- is a suite of automated docking tools for predicting the bound conformations of flexible ligands to macromolecular targets. It is designed to predict how small molecules of substrates or drug candida...

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...d were purchased from Sigma Chemical Co. (St. Louis, MO, USA). Software The Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIH P41 RR-01081), was used for structure preparation and visualization (17). Reduce was used for adding hydrogens to the receptor Protein Data Bank molecular structure files (18). Ligand conformational searches for X-ray ligands were made with VEGA 2.2.0 (19). Docking studies were carried out with Autodock 4.0 and AutoDockTools4 (Scripps Research Institute, La Jolla, CA, USA) (20). AutoDock4 evaluates the energies for both the bound and unbound states and uses a semi-empirical free energy force field by taking into account hydrogen bonding, electrostatic interactions, deviation from covalent geometry, internal ligand torsional constraints, and desolvation effects (20). On average, a standard error of about 2–3 kcal ⁄ mol in prediction of binding free energy in cross-validation studies was found, and this was found to be good enough to differentiate between nm, lM, and mM activities of leads (20). ACD ⁄ ChemSketch was used to generate Simplified Molecular Input Line Ent...

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.... Fortunately, with the increasing development of computer technology, high throughput virtual screening gives us such ability to generate sufficient data. As a result, molecular docking by AutoDock4 =-=[57]-=- was adopted to simulate the interactions between natural products and cellular targets. 4. Network Pharmacology Network pharmacology was proposed by Hopkins [58,59] in 2007 and it could take advantag...

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...mplex analytical procedures. The NBCR web server http://ws.nbcr.net contains a registry of several classes of biomedical application services, including docking and virtual screening using Autodock 4 =-=(3)-=- and Autodock Vina (4); electrostatics analysis using PDB2PQR (5,6) and APBS *To whom correspondence should be addressed. Tel: +1 858 246 0336; Fax: +1 858 822 1619; Email: j2ren@ucsd.edu Corresponden...

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...ential for 3 polar contacts, with one in the adenine pocket. A dihedral angle of 130° is rotated 180 degrees and had potentially four polar contacts, with two in the adenine pocket. We used AutoDock4 =-=(35, 36)-=- to predict a binding mode of PP242 to TOR (Figure 8, panel A), using compound S2 (Supplementary Figure S2) crystallized in human PI3KC� (RCSB, PDB 3ene) to define a starting position. All of the resi...

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...onformation in response to ligand binding [15]. In order to rationalize the binding mode of theonellasterol on FXR receptor, we have therefore performed docking calculations (by Autodock 4.2 software =-=[16]-=-) on several FXR structures co-crystallized with different compounds [17–20] with the aim to predict the position of the LBD in complex with theonellasterol. As reported, the activation of the FXR by ...

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...of 5.0 kcal mol 21 A˚ 22 ). Each simulation was continued for 500 ns without any restraints. Docking simulations Docking simulations of AMPPCP to the ATP-binding site were performed with AutoDock 4.2 =-=[40]-=-. Grid maps of 2.562.562.5 nm representing the protein were centered on the ATP-binding site. During docking simulations, both AMPPCP and SERCA were kept rigid; and the conformation of AMPPCP was kept...

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....cam.ac.uk/ ~rapper/rampage.php; Lovell et al., 2003). The structures of the LBP of the CAR1 structure (Xu et al., 2004) and the Phyre generated CAR2 and CAR3 models were then characterized using Pocket-Finder (http://bmbpcu36.leeds .ac.uk/pocketfinder/) (Laurie and Jackson, 2005). ICM MolSoft Browser Pro 382 DEKEYSER ET AL. by guest on January 25, 2012 http://toxsci.oxfordjournals.org/ D ow nloaded from (http://www.molsoft.com/) was used to visualize CAR and CAR3 predicted structures and CAR1 models and LBP. For the docking simulations of DEHP into the Phyre CAR2 structural model, AutoDock4 (Morris et al., 2009) and AutoDock Vina (Trott and Olson, 2010) were used with AutoDockTools graphical user interface. Prior to docking, all polar hydrogens were added to the molecules. The ligands were allowed to rotate freely around all active torsions during docking, whereas the protein structures remained rigid. A 223 223 22 A grid box was used to center the docking algorithm on the ligand-binding site. All other settings were defaults in AutoDock Vina. The resulting ligand-docking configurations were analyzed for lowest binding energy (kilocalories per mole) and visualized using and Molsoft Browser Pro. Stat...