Difference between revisions of "2016 DOCK tutorial with Beta Trypsin"
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For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. Use this link [http://www.mediawiki.org/wiki/Help:Formatting Wiki Formatting] as a reference for editing the wiki. This tutorial was developed collaboratively by the AMS 536 class of 2014, using DOCK v6.6. | For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. Use this link [http://www.mediawiki.org/wiki/Help:Formatting Wiki Formatting] as a reference for editing the wiki. This tutorial was developed collaboratively by the AMS 536 class of 2014, using DOCK v6.6. | ||
| − | ==I. Introduction== Yaping She | + | ==I. Introduction== |
| + | Yaping She | ||
===DOCK=== | ===DOCK=== | ||
| Line 14: | Line 15: | ||
| − | ==II. Preparing the Receptor and Ligand== Beilei Jiang | + | ==II. Preparing the Receptor and Ligand== |
| + | Beilei Jiang | ||
| − | ==III. Generating Receptor Surface and Spheres== Lauren Prentis | + | ==III. Generating Receptor Surface and Spheres== |
| + | Lauren Prentis | ||
| Line 30: | Line 33: | ||
| − | ==IV. Generating Box and Grid== Monaf Awwa | + | ==IV. Generating Box and Grid== |
| + | Monaf Awwa | ||
| Line 41: | Line 45: | ||
| − | ==V. Docking a Single Molecule for Pose Reproduction== Agatha Lyczek & Haoyue Giuo | + | ==V. Docking a Single Molecule for Pose Reproduction== |
| + | Agatha Lyczek & Haoyue Giuo | ||
| Line 61: | Line 66: | ||
| − | ==VI. Virtual Screening== Katie Maffucci | + | ==VI. Virtual Screening== |
| + | Katie Maffucci | ||
===DOCK Preparation=== | ===DOCK Preparation=== | ||
Revision as of 12:11, 9 March 2016
For additional Rizzo Lab tutorials see DOCK Tutorials. Use this link Wiki Formatting as a reference for editing the wiki. This tutorial was developed collaboratively by the AMS 536 class of 2014, using DOCK v6.6.
Contents
I. Introduction
Yaping She
DOCK
Beta Trypsin
Organizing Directories
II. Preparing the Receptor and Ligand
Beilei Jiang
III. Generating Receptor Surface and Spheres
Lauren Prentis
Generating the Receptor Surface
Placing Spheres
IV. Generating Box and Grid
Monaf Awwa
Box Generation
Grid computing
V. Docking a Single Molecule for Pose Reproduction
Agatha Lyczek & Haoyue Giuo
Minimization
Rigid docking
Flexible Docking
VI. Virtual Screening
Katie Maffucci
