Contents
Release 2005, March 2005
1. Introduction
- What is Affinity?
- How Is It Different from Other Docking Methods?
- Comparison with Interactive Docking
- Comparison with Other Docking Methods in the Literature
- What Is It Intended For?
- Why Is It Necessary?
- How Do I Use Affinity?
- Program Overview
- Acknowledgment and References
2. Theory and Implementation
- Overview
- Energy and Penalty Terms
- 1) Grid Based Methods for Nonbond Interactions and Solvation Effects
- Grid Representation of Bulk Atoms
- Approximations for CFF9x Forcefields
- Exact Treatment of Interactions among Movable Atoms
- Solvation Parameter Assignment
- Using the Same Grids for Different Ligands
- Implementation of the MM/Grid method
- Setup Grids
- Discover/Grid Calculation
- 2) Other Nonbond Methods
- 3) Geometric Restraints:
- a) Hydrogen Bond Contacts
- b) Ligand Confinement
- c) Tethering
- Note on GridDocking
- Docking Procedure
3. Command Summary
- Affinity Pulldown
- GridDocking
- Setup_Grids
- Minimize
- Dynamics
- Setup_System
- Setup_Torsion
- SA_Docking
4. Methodology
- General Procedure
- Preparing System
- Performing the Calculation
- Analyzing Results
- Computing Ligand/Receptor Interaction Energy
- Advanced Procedures
- Using Monte Carlo Dynamics for Docking in GridDocking
- Using the Same Grids for Different Ligands in GridDocking
- Using Local Solvation Parameters
- Using GridDocking Without Solvation
- Using a Local Docking Script
- Modifying Discover Input
5. Tutorial
A. References
B. Glossary
C. File Formats
- Cartesian Coordinate File (.car)
- Molecular Data File (.mdf)
- Command Input File (.inp)
- Input File for SA_Docking
- Input File for GridDocking
- Solvation Template Files
- COORD.res File
- NONBOND.param File
- Grid Files (.grd) for GridDocking
- Torsion File (LIG_TOR) for Setup_Torsion
- Main output file from Discover (.out)
Last updated November 22, 2003.
Copyright © 2003, Accelrys Inc. All rights
reserved.