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 & Omar Sanchez Reyes


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