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

DOCK

Thrombin

Organizing Directories

II. Preparing the Receptor and Ligand

III. Generating Receptor Surface and Spheres

Generating the Receptor Surface

Placing Spheres

IV. Generating Box and Grid

Box Generation

Grid computing

V. Docking a Single Molecule for Pose Reproduction

Minimization

Rigid docking

Flexible Docking

VI. Virtual Screening

Small Scale Virtual Screen

Large Scale Virtual Screen

VIII. Frequently Encountered Problems

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