Table of Contents

Introduction

• Acknowledgments
• Installation
• Generalized DOCK Schematic
• Detailed DOCK Map
• Overview of the DOCK program suite
  • General Concepts
  • Specific Concepts
  • Caveats
  • Programs and References
  • Bibliography

Beginner's Guide

• Scope of This Guide
• What DOCK Can Do for You
• Basic DOCK References
• Overview of the DOCK package
• A Caution Concerning Disk Space
• Preparing for a DOCK Run
  • Working With Macromolecular Models and Generating the Molecular Surface
  • Representing the Site With Spheres
  • Creating the Scoring Grids
  • Preparing Ligand Molecules
  • Labeling Atoms and Spheres for Chemical Matching
• Running DOCK
  • Setting Up Directories
  • Creating INDOCK
  • Starting a DOCK Run
  • Restarting a Search Run
  • Looking at the Results

DOCK Reference Manual

• DOCK
  • What's New in DOCK 3.5
  • sphgen
  • distmap
  • chemgrid
  • dock3.5
• New Features
  • Chemical Matching
  • Force-Field Score Optimization
  • Degeneracy Checking
  • Critical Clusters
  • Ligand Mirroring
• Docking Examples
  • 3dfr
• Database Preparation
  • File Format Interchange
  • dbprocess
  • sdf2mol2, sybdb
  • mkdb
  • mol2db
  • dock 3.5 ligand database format
  • dock 3.0 ligand database format
• Accessories
  • Organizer
• References

Appendices

• Appendix 1: Ligand File Formats
  • Extended PDB format
  • SYBYL MOL2 format
  • DOCK database format, version 2.1: from mkdb
  • DOCK database format, version 3.0: from convsyb
  • DOCK database format, version 3.5: from mol2db
• Appendix 2: Parameter Files
  • vdw.parms.amb
  • vdw.parms.amb.mindock
• Appendix 3: Contact Information
  • Molecular Design Limited - ACD
  • Tripos - SYBYL
  • Biosym - Insight, Delphi
  • QCPE - MS
  • Cambridge - CSD
  • Brookhaven Protein Data Bank
  • UCSF MidasPlus
  • AMBER
  • Goodford's GRID
  • Other Web Resources

Index