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Table Of Contents

Homology Model: Template Selection
DockoMatic 2.0 GUI
DockoMatic: Accessing the TIM Wizard
DockoMatic – TIM Wizard Interface
TIM Step 1: Enter Template Sequence
TIM Step 2: Search for a Template
TIM Step 3: Sequence Alignment
TIM Step 3: Select Aligned Sequence
TIM Step 4: Edit Aligned Sequence
TIM Step 5: Model Generation
TIM Step 5: List of Models Created
TIM Step 5: Select Homology Model
End TIM Wizard: 3D Model for MD
Location of Model Structure Files
HM Validation: Ramachandran Plot
HM Validation: Sequence Alignment
HM Validation: Structure Overlay
Molecular Docking in DockoMatic
MD: Getting Started
MD Step 1: Selecting a Ligand
MD Step 2: Receptor Selection
MD Step 3: Receptor Binding Site Selection
Site Selection
MD Step 4: Job Setup
MD: Job Status
MD: Starting the Docking Jobs
Review Files in Terminal Window
Protein Data Base File for Arixtra
Viewing the Contents of a Grid Parameter File
Viewing the Contents of a Docking Parameter File
DockoMatic: Grid Parameter Files
DockoMatic: Job Status in Terminal
MD Result Analysis: Cluster Histogram
Viewing MD Results
MD Result Analysis: Visualization
MD Analysis: Selecting a Result
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Published by Abdurrahman Olğaç
Student Tutorial
Student Tutorial

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Categories:Types, Presentations
Published by: Abdurrahman Olğaç on Jan 10, 2014
Copyright:Attribution Non-commercial


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