Using DOCK o characterize protein ligand interactions使用Dock表征蛋白质配体相互作用.pptVIP

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Using DOCK o characterize protein ligand interactions使用Dock表征蛋白质配体相互作用.ppt

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Using DOCK o characterize protein ligand interactions使用Dock表征蛋白质配体相互作用

Using DOCK to characterize protein ligand interactions Sudipto Mukherjee Robert C. Rizzo Lab Acknowledgements The Rizzo Lab Dr. Robert C. Rizzo Brian McGillick Rashi Goyal Yulin Huang Support Stony Brook Department of Applied Mathematics and Statistics New York State Office of Science, Technology Academic Research Computational Science Center at Brookhaven National Laboratory National Institutes of Health (NIGMS) NIH National Research Service Award. Grant Number:1F31CA134201-01. (Trent E. Balius) IBM Rochester Carlos P. Sosa Amanda Peters Introduction What is Docking? Compilation of DOCK on BG Scaling Benchmarks Docking as a Drug Discovery Tool Receptor: Trypsin Ligand: Benzamidine Complex Docking : Computational Search for energetically favorable binding poses of a ligand with a receptor. Find origins of ligand binding which drive molecular recognition. Finding the correct pose, given a ligand and a receptor. Finding the best molecule, given a database and a receptor. Conformer Generation Shape Fitting Scoring Functions Pose Ranking Docking Resources Small Molecule Databases NCI (National Cancer Institute) UCSF ZINC Protein receptor structure Protein Data Bank / Docking Tutorials Rizzo Lab Wiki /index.php/DOCK_tutorial_with_1LAH UCSF Tutorials /DOCK_6/index.htm AMS535-536 Comp Bio Course Sequence Modeling Tools Chimera (UCSF) Compiling DOCK6 on BlueGene IBM XL Compiler Optimizations O5 Level Optimization qhot Loop analysis optimization qipa Enable interprocedural analysis PowerPC Double Hummer (2 FPU) qtune=440 qarch=440d MASSV Mathematical Acceleration Subsystem -lmassv DOCK Accessory programs not ported Energy Grid files must be computed on FEN, not on regular Linux cluster because of endian issues High Throughput Computing Validation for Drug Discovery Using the DOCK Program on a Massively Parallel System Thanks to Amanda Peters, Carlos P. Sosa (IBM) for compilation help Compiling Dock on BG/L Cross-compile on Front End Node with Makefile param