2016 DOCK tutorial with Beta Trypsin

From Rizzo_Lab

Revision as of 16:29, 15 February 2016 by Stonybrook (talk | contribs) (2016 DOCK tutorial with Thrombin moved to 2016 DOCK tutorial with Beta Trypsin)

(diff) ←Older revision | view current revision (diff) | Newer revision→ (diff)

Jump to: navigation, search

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

1 I. Introduction
2 II. Preparing the Receptor and Ligand
3 III. Generating Receptor Surface and Spheres
- 3.1 Generating the Receptor Surface
- 3.2 Placing Spheres
4 IV. Generating Box and Grid
- 4.1 Box Generation
- 4.2 Grid computing
5 V. Docking a Single Molecule for Pose Reproduction
6 VI. Virtual Screening
- 6.1 DOCK Preparation
- 6.2 Post Processing
7 VIII. Frequently Encountered Problems

I. Introduction

DOCK

Beta Trypsin

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

DOCK Preparation

Post Processing

VIII. Frequently Encountered Problems

Retrieved from "https://ringo.ams.stonybrook.edu/index.php?title=2016_DOCK_tutorial_with_Beta_Trypsin&oldid=9559"