FRED
Fast Rigid Exhaustive Docking
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Front Matter
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FRED Fast Rigid Exhaustive
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1. Version
Contents
1. Version
2. Introduction
2.1 Overview
2.2 Key technologies
3. Installation and Platform Notes
3.1 Licenses
3.2 Installation
3.2.1 Linux/Unix
3.2.2 Windows
3.2.3 OS X
3.3 PVM
3.3.1 PVM hosts file
3.3.2 PVM Scaling
4. Theory
4.1 Input
4.2 Docking
4.2.1 Exhaustive Docking
4.2.2 Optimization
4.2.3 Consensus Structure
4.2.4 Force Field Refinement
4.3 Scoring
4.3.1 Overview
4.3.2 Shapegauss
4.3.3 PLP
4.3.4 Chemgauss2
4.3.5 Chemgauss3
4.3.6 Chemscore
4.3.7 OEChemscore
4.3.8 Screenscore
4.3.9 Zapbind
4.3.10 CGO
4.3.11 CGT
4.3.12 Multiple Active Site Correction
4.4 Output
4.4.1 Docked molecules
4.4.2 Undocked molecules
5. Running FRED
5.1 Specifying Parameters
5.2 Command Line Help
5.3 Receptor file
5.3.1 File Format
5.3.2 Querying
5.3.3 GUI Creation
5.3.4 Command Line Creation
5.4 Constraints
5.4.1 Protein constraints
5.4.2 Custom constraints
5.5 Preparing ligand database
5.5.1 Protonation state
5.5.2 Charging molecules
5.5.3 Generating conformers
5.6 Screen output
5.7 Complete list of output files
5.7.1 Setup File
5.7.2 Status File
5.7.3 Information message log
5.7.4 Warning log
5.7.5 Receptor file
5.7.6 Score Files
5.7.7 Docked Structure Files
5.7.8 Alternate Score Files
5.7.9 Alternate Docked Structure Files
5.7.10 Consensus Hitlist
5.7.11 MASC Consensus Hitlists
5.7.12 Undocked Ligand Files
6. Example Command Lines
6.1 Simple command lines
6.1.1 Docking with an existing receptor
6.1.2 Creating a receptor and docking
6.1.3 Changing the output file format
6.1.4 Setting a prefix and/or an output directory
6.2 Creating a receptor
6.2.1 With a box
6.2.2 With a bound ligand
6.2.3 With a box and a bound ligand
6.2.4 Without a box or bound ligand
6.3 Finding the right pose
6.3.1 Rescoring - scoring without docking
6.3.2 Setting the exhaustive scoring and optimization functions
6.3.3 Adjusting consensus structure - changing weights
6.3.4 Turning consensus structure off
6.4 Scoring
6.4.1 One scoring function
6.4.2 Multiple scoring functions
6.5 Using MASC
6.5.1 Scoring with MASC
6.5.2 Using multiple MASC and other scoring functions
6.5.3 Preparing ligands
6.5.4 Preparing ligands with your own reference sites
6.5.5 Preparing ligands
6.6 Ligand+Structure based design
6.6.1 Scoring with ligand based design
6.6.2 Docking and scoring with ligand based design
7. Parameters
7.1 Execute Options
7.2 Input Ligands
7.2.1 MASC Preparation
7.3 Receptor Site
7.3.1 Creating Receptor Site
7.4 Docking
7.4.1 Exhaustive Search
7.4.2 Optimization
7.4.3 Consensus Structure
7.4.4 Force Field Refinement
7.5 Scoring
7.5.1 Standard Scoring Functions
7.5.2 MASC Scoring Functions
7.6 Output
A. Release Notes
A.1 FRED 2.2.4 Change Log
A.2 FRED 2.2.3 Change Log
A.3 FRED 2.2.2 Change Log
A.4 FRED 2.2.1 Change Log
A.5 Initial FRED 2.2 release
A.5.1 New Features / Improvements
A.5.2 Changes
B. File formats
B.1 Valid file extensions for Both Reading and Writing
B.2 Valid File Extensions for Reading
B.3 Valid File Extensions for Writing
C. Glossary
D. Standard MASC reference sites
E. FRED 1.2.10 to FRED 2.1 parameter dictionary
E.1 Parameter_Input
E.2 PVM
E.3 Molecule_Loader
E.4 Output
E.5 Omega
E.6 Receptor
E.6.1 FRED
E.6.2 Sequential_Screen
F. FRED 2.0 to FRED 2.2 parameter dictionary
G. FRED 2.1 to FRED 2.2 parameter dictionary
H. Accessing scores in oeb files from OEChem
H.1 Overview
H.2 Tags
Bibliography
FRED
Fast Rigid Exhaustive Docking
Previous:
Front Matter
Up:
FRED Fast Rigid Exhaustive
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1. Version
Documentation released on August 12, 2008.
