Jan 18 2018 Feedback.
Contents
 
Introduction
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
Learn and Predict
Docking
Virtual Screening
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index

ICM-Pro User Guide v.3.8

by Ruben Abagyan, Andrew Orry, Eugene Raush, and Maxim Totrov
Copyright © 2017



Jan 18 2018

Feedback.

Table of contents

Introduction
Reference Guide
2.1 Graphics Reference Guide
2.2 ICM-Browser-Pro Reference Guide
2.3 ActiveICM Reference Guide - Create 3D Molecular Documents for the Web and PowerPoint
2.4 ICM-Chemist Reference Guide
2.5 ICM-Chemist-Pro Reference Guide
2.6 Menu Option Guide
2.7 Tab Guide
Getting Started
3.1 The Basics of the Graphical User Interface
3.2 How to search and download Protein Structure, Sequences, and Chemicals
3.3 Create New Objects
3.4 Open and Read Files
3.5 Saving Files
3.6 Making Selections
3.7 Preferences
Protein Structure
4.1 Convert to ICM Object
4.2 Pocket Display
4.3 Crystallographic Analysis
4.4 Protein Superposition
4.5 Protein Structure Analysis
4.6 3D Predict
Molecular Graphics
5.1  Molecule Representation
5.2  Multi-Windows
5.3  Meshes - Surface - Grobs
5.4  Coloring
5.5  Lighting
5.6  3D Stereo
5.7  3D Printing
5.8  Labeling and Annotation
5.9  Display Distances and Angles
5.10 Graphics Effects
5.11 Graphics Shortcuts
5.12 Molecule Move Buttons
5.13 Clipping Tools
5.14 Graphic Layers
5.15 High Quality Publication Images
5.16 Movie Making
Slides & ActiveICM
6.1  Making Slides
6.2  Make a Movie from a Set of Slides
6.3  How to View and Navigate Slides
6.4  How to Edit Slides
6.5  How to Add Smooth Blending and Transition Effects Between Slides
6.6  How to Make Molecular Documents - Link HTML Text to Slides
6.7  ActiveICM
6.8  How to Embed in Microsoft PowerPoint 2003
6.9  How to Embed in Microsoft PowerPoint 2007
6.10 How to Embed in MicroSoft PowerPoint 2010
6.11 Embed in Web Browser
6.12 How to Use ActiveICM in PowerPoint
6.13 How to Change ActiveICM Component Properties
6.14 Advanced use of activeICM: Macros to direct visualisation changes
6.15 Background Images
6.16 ICM JavaScript (IcmJS)
Working with Sequences and Alignments
7.1 Read and Save Sequences
7.2 Sequence Secondary Structure
7.3 Bioinfo Menu
7.4 BLAST Search
7.5 Sequence Editor
7.6 Sequence Alignments
7.7 Alignment Editor
7.8 Color Structure and Surface by Alignment
Protein Modeling
8.1  Homology Modeling
8.2  Loop Modeling
8.3  Design Loop
8.4  Graft Loop
8.5  Loop Preferred Residues
8.6  Find Loops in PDB
8.7  Regularization
8.8  Refine Side Chains
8.9  Making a disulfide bond.
8.10 Making a Mutation
8.11 Modify Amino Acid
8.12 Predicting Change in Binding Free Energy upon Mutation
8.13 Predicting Change in Protein Stability upon Mutation
8.14 Effect of Mutation on Protein-Peptide
8.15 Effect of Mutation on Protein Ligand Binding
8.16 Predict Disulfide Bond
8.17 Protein Sculpting
8.18 Sample Protein
8.19 Sample Peptide
8.20 Molecular Mechanics
Cheminformatics
9.1  Read Chemical Structures
9.2  Save Chemical Structures and Images
9.3  Working with Chemical Spreadsheets.
9.4  Molecular Editor
9.5  Chemical Search
9.6  2D Ligand Interaction Diagram
9.7  Convert Chemicals to 3D
9.8  Generating Chemical Fragments
9.9  Find Bioisostere
9.10 Molcart
9.11 Calculate Properties
9.12 Standardize Table
9.13 Annotate By Substructure
9.14 Align/Color by 2D Scaffold
9.15 Set Formal Charges
9.16 Enumerate Formal Charge States
9.17 Convert
9.18 Build Prediction Model
9.19 Predict
9.20 Generate 3D Conformers
9.21 Generate Tautomers
9.22 Generate Stereoisomers
9.23 Prodrug
9.24 Ligand Energetics
9.25 Cluster Set
9.26 PCA Analysis
9.27 Maximum Common Substructure (MCS) Dendrogram
9.28 Compare Two Sets
9.29 Merge Two Sets
9.30 Select Duplicates
9.31 Multi Parameter Optimization
9.32 Combinatorial Chemistry
9.33 SAR Analysis
9.34 Substructure Superposition
9.35 Atomic Property Field Superposition
9.36 APF Tools
10 Learn and Predict
10.1 Learn
10.2 Predict
10.3 Fingerprint Methods
10.4 3D QSAR
10.5 A Little Theory on Learning
11 Docking
11.1 Small Molecule Docking
11.2 Induced Fit (Flexible) Docking
11.3 Template Docking
11.4 Covalent Docking
11.5 ICM X-Ray AutoFit - Automated Model Building into Density
11.6 Protein-Protein Docking
12 Virtual Ligand Screening
12.1 Virtual Ligand Screening
12.2 Fragment Screening
12.3 Ligand-Based Screening using APF 3D Pharmacophores
13 MolScreen
13.1 Model Types
13.2 Brief Panel
13.3 Full Model Panel
13.4 Custom Model Panel
13.5 Results Table
13.6 Make Chemical Classification Model
13.7 Make APF Docking SAR Model
13.8 Predict Metabolic Oxidation
14 The 3D Fully Interactive Ligand Editor
14.1  Setup Ligand and Receptor
14.2  Ligand-Editor-Preferences
14.3  Display Options
14.4  Evaluate Ligand Score and Strain
14.5  Edit Ligand
14.6  Virtual Screen: Find Best Replacement Group
14.7  Multiple Position Group Scan
14.8  Dock or Minimize Ligand
14.9  Dock from Table
14.10 Fragment Linking
14.11 Impose Tethers or Distance Restraints
14.12 Docking Templates
14.13 Defined Flexible Receptor Groups
14.14 Side Chain Refinement
14.15 Multiple Receptor Docking
14.16 Covalent Docking in the Ligand Editor
14.17 Dock to Atomic Property Fields
14.18 How to Save Ligand Receptor Complex as PDB
14.19 Export Docking Project.
14.20 Close and Clean Up Project
15 Working with Tables and Plots
15.1 Standard ICM Tables
15.2 Molecular Tables
15.3 Insert Interactive Objects into Table Cell
15.4 Plotting Table Data
15.5 Principal Component Analysis
15.6 Learn and Predict
15.7 Data Clustering
16 Working with Local Databases
16.1 How to make a local database.
16.2 Browse Database
16.3 Edit Database
16.4 Query Local Database
17 ICM-Scarab - Data Capture, Integrator and Miner
17.1 Scrab Installation
17.2 Upload Data
17.3 Query Metadata
17.4 Browse and Export Data
17.5 Add a New User
17.6 Create a New Project and Assign User
17.7 Pages
18 ICM in KNIME
19 Tutorials
19.1  Graphics Tutorials
19.2  Creating Fully Interactive Slides for PowerPoint and the Web Tutorial
19.3  Protein Structure Tutorials
19.4  Sequence and Alignment Tutorials
19.5  Protein Modeling Tutorials
19.6  Cheminformatics Tutorials
19.7  3D Ligand Editor Tutorial
19.8  Atomic Property Field Tutorials
19.9  Ligand Docking Tutorials
19.10 Protein-Protein Docking Tutorial using FFT Method
19.11 Virtual Ligand Screening Tutorials
19.12 Induced Fit (Flexibility) Docking Tutorials
19.13 Chemical FingerPrint QSAR Model Tutorial
19.14 3D QSAR Tutorial
20 Frequently Asked Questions
20.1  FAQ Installation and Troubleshooting
20.2  FAQ Graphics and Display
20.3  FAQ ActiveICM
20.4  FAQ Structure
20.5  FAQ-Docking
20.6  FAQ-Sequences and Alignments
20.7  FAQ-Modeling
20.8  FAQ-Cheminformatics
20.9  FAQ-MolCart
20.10 FAQ-Script

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