Contents
Release 2005, March 2005
1. Introduction
- What is Modeler?
- Development
- The Insight II interface and Modeler
- Pilot tutorials
- MODELER standalone
2. Theory of comparative modeling
- Background
- Structure alignment
- Sequence-structure alignment
- Building the structure
- Probability density functions
- Probability density functions observed in known protein structures
- Probability density functions for bond lengths, bond angles and dihedrals
- Atom-atom repulsions
- Distance between two Ca atoms
- Distance between main chain N and O atoms
- Distances between sidechain-sidechain and sidechain-mainchain atoms.
- Main chain conformation
- Side Chain conformation restraints
- Restraining chi1 side chain dihedral angles
- Restraining chi2 dihedral angles
- Restraining chi3 dihedral angles
- Restraining chi4 dihedral angles
- Basis and feature probability density functions
- Feature PDFs used for restraining model protein features
- Ca-Ca distance feature PDF
- Main chain N-O distance feature PDF
- Stereochemical feature PDF
- Main chain conformation feature PDFs
- Side Chain dihedral angle feature PDFs
- Molecular PDF used for structure generation
- Structure Generation using Modeler
- Modeling loops
3. Methodology & Implementation
- Basic algorithm
- Sequence alignment
- Model calculation
- Model refinement
- Evaluating Modeler results
- The Modeler control file
- Modifying files to modify models
- Using user-defined residue types
- Sequence window
- Sequence display
- Controls
- Sequence boxes
- Sequence gaps
- Manipulating the sequence display
- Scrolling modes
- Seq mode
- Box mode
4. Command Summary
- Sequences pulldown
- Boxes pulldown
- Background_Job pulldown
- Modeler pulldown
A. References
B. File Formats
- Alignment file
- Restraint file (.rsr extension)
- Job control file
- Spreadsheet table files
- Modeler files
Last updated November 22, 2003.
Copyright © 2003, Accelrys Inc. All rights
reserved.