2016 DOCK tutorial with Beta Trypsin

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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.

==I. Introduction== Yaping She


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


Rigid docking

Flexible Docking

==VI. Virtual Screening== Katie Maffucci

DOCK Preparation

Post Processing

VIII. Frequently Encountered Problems