| QUANTA 2006 Protein Design |
Overviewing the Protein Design palette
Protein MODELER
1. The Sequence Viewer
Overview
Sequence Data
Saving Sequences And Alignment Between Sessions
Changing Maximum Number of Sequences
The Sequence Viewer
Display of Graphs
The Sequence Viewer icons
2. Reading and Writing Sequence Data Files
Overview
Reading and Writing Sequence Data Files
Read Sequence/Alignment File
Read Sequence Data File
Demo of User Data
To run the demo:
Reference
Write Sequence File
Plot Sequence Viewer
Remove Sequence
3. Protein Utilities
Overview
Simple Representations of Proteins
Tools and Options
Color by Structure Properties
Color By Sequence Properties
Color by Homology
4. Protein Editor
Overview
Editing Proteins
Ideal Residue Definitions
Regularization
Residues
Editing Segments
Hydrogen Addition
Tools and Options
Amino Acid Selection
The Editing Tools
4. Predict Secondary Structure
Overview
Predicting Secondary Structures
Momany Prediction
Holley/Karplus Prediction
GOR Prediction
Conservation Profiles
Hydrophobicity Scales
Sequence Viewer Plots
Saving Predictions
Tools
5. Align and Superpose
Overview
Aligning and Superposing Sequences
Using Active Sequences and Active Ranges
Criteria for Aligning and Matching Sequences
Alignment
Manual Alignment Editing
Saving and Restoring Alignments
Dot Plots
Alignment Constraints
Matching Residues
Color by Homology
Superposing Structures
Tools and Options
The Constraints Palette
Constraint Palette Tools
6. Create Homology Model
Overview
Copying Homology
Tools
7. Superpose Folding Motif
Overview
Superposing Folding Motifs
Protein Geometry
Secondary Structure Representation
Sequence Alignment
Tools and Options
Select Active Secondary Structure
Match Secondary Structure
Reviewing the Matches
Superpose and Align Molecules
Demonstration of Using Superpose Motif
8. Model Backbone
Overview
Modeling the Protein Backbone
Regularizing Regions
Folding Residues
Fragment Searching
Tools and Options
9. Model Side Chains
Overview
Modeling Sidechains
Close Contacts
Rotamers
Spinning Side Chains
Tools and Options
10. Analyze Secondary Structure
Overview
Analyzing Secondary Structures
Hydrogen Bond Calculations
Secondary Structure Assignment
Tools and Options
11. Calculate Accessibility
Overview
Reference
Calculating Accessibility
Accessibility Calculations
Contact Area
Displaying Accessibility and Contact Areas
Tools and Options
12. Display Contact Maps
Overview
Calculating Contact Maps
Plotting Method
Secondary Structure Elements
Molecule Display
Difference Contact Maps
Distance Contact Maps
Energy Contact Maps
Interaction-Type Contact Maps
Hydrogen Bonds
Residue Type
Tools and Options
13. Analyze Domain Structure
Overview
Analyzing Domain Structures
The Clustering Algorithm
Loop Regions
Tools and Options
14. Profile Analysis
Overview
Analyzing Protein Profiles
Comparing a Profile to a Sequence
Plotting Profiles
Comparing Profiles to Other Sequences
Tools and Options
15. Protein Information
Overview
Retrieving Protein Information
Tools
Running a Protein Information Query
16. Sequence Database
Overview
FASTA Sequence Searching
Tools
17. Structural Database
Overview
Searching the Structure Database
Defining A Structure Database Query
Tools and Options
18. Motif Database
Overview
Searching the Motif Database
Tools and Options
Motif Database Log File
19. Protein Health
Overview
Using Protein Health
Analysis of Multiple Conformations
Tools and Options
Dunbrack and Karplus rotamer definitions
20. Using MODELER
Overview
MODELER
Accessing MODELER
Displaying MODELER results
Evaluating MODELER Results
Deleting files after a MODELER run
MODELER files and file modifications
The MODELER control file
Modifying files to modify models
Defining MODELER Restraints
MODELER Theory
Sequence-structure alignment (Align2D)
Structure alignment (Align3D)
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
References
A. Conversion of External Sequence Data Files to QUANTA Format
Sequence Data File Format
Sequence User Color File Format
B. Creating a Fragment dmfile
Overview
The PDB Master File
Running CREBASE to create the Database Files
Creating the MSF Library
D. The Geometric Structure Definition File
The file format
E. The Protein Parameter File
Overview
Pearson (FASTA) format (extension .aa)
GCG (extension .gcg)
HAHU
NBRF-PIR
SWISSPROT (extension .sws)
G. Running the Search Standalone
Overview
Search Commands
Running a Search
H. Torsion Angles and Centers
Overview
Database file format
I. Wildcard Residue Type File