Sep 13 2018 Feedback.
Contents
 
Introduction
Help Videos
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



Sep 13 2018

Feedback.

Table of contents

Introduction
Help Videos on YouTube
Reference Guide
3.1 Graphics Reference Guide
3.2 ICM-Browser-Pro Reference Guide
3.3 ActiveICM Reference Guide - Create 3D Molecular Documents for the Web and PowerPoint
3.4 ICM-Chemist Reference Guide
3.5 ICM-Chemist-Pro Reference Guide
3.6 Menu Option Guide
3.7 Tab Guide
Getting Started
4.1 The Basics of the Graphical User Interface
4.2 How to search and download Protein Structure, Sequences, and Chemicals
4.3 Create New Objects
4.4 Open and Read Files
4.5 Saving Files
4.6 Making Selections
4.7 Preferences
Protein Structure
5.1 Convert to ICM Object
5.2 Pocket Display
5.3 Crystallographic Analysis
5.4 Protein Superposition
5.5 Protein Structure Analysis
5.6 3D Predict
Molecular Graphics
6.1  Molecule Representation
6.2  Multi-Windows
6.3  Meshes - Surface - Grobs
6.4  Coloring
6.5  Lighting
6.6  3D Stereo
6.7  3D Printing
6.8  Labeling and Annotation
6.9  Display Distances and Angles
6.10 Graphics Effects
6.11 Graphics Shortcuts
6.12 Molecule Move Buttons
6.13 Clipping Tools
6.14 Graphic Layers
6.15 High Quality Publication Images
6.16 Movie Making
Slides & ActiveICM
7.1  Making Slides
7.2  Make a Movie from a Set of Slides
7.3  How to View and Navigate Slides
7.4  How to Edit Slides
7.5  How to Add Smooth Blending and Transition Effects Between Slides
7.6  How to Make Molecular Documents - Link HTML Text to Slides
7.7  ActiveICM
7.8  How to Embed in Microsoft PowerPoint 2003
7.9  How to Embed in Microsoft PowerPoint 2007
7.10 How to Embed in MicroSoft PowerPoint 2010
7.11 Embed in Web Browser
7.12 How to Use ActiveICM in PowerPoint
7.13 How to Change ActiveICM Component Properties
7.14 Advanced use of activeICM: Macros to direct visualisation changes
7.15 Background Images
7.16 ICM JavaScript (IcmJS)
Working with Sequences and Alignments
8.1 Read and Save Sequences
8.2 Sequence Secondary Structure
8.3 Bioinfo Menu
8.4 BLAST Search
8.5 Sequence Editor
8.6 Sequence Alignments
8.7 Alignment Editor
8.8 Color Structure and Surface by Alignment
Protein Modeling
9.1  Homology Modeling
9.2  Loop Modeling
9.3  Design Loop
9.4  Graft Loop
9.5  Loop Preferred Residues
9.6  Find Loops in PDB
9.7  Regularization
9.8  Refine Side Chains
9.9  Making a disulfide bond.
9.10 Making a Mutation
9.11 Modify Amino Acid
9.12 Predicting Change in Binding Free Energy upon Mutation
9.13 Predicting Change in Protein Stability upon Mutation
9.14 Effect of Mutation on Protein-Peptide
9.15 Effect of Mutation on Protein Ligand Binding
9.16 Predict Disulfide Bond
9.17 Protein Sculpting
9.18 Sample Protein
9.19 Sample Peptide
9.20 Molecular Mechanics
10 Cheminformatics
10.1  Read Chemical Structures
10.2  Save Chemical Structures and Images
10.3  Working with Chemical Spreadsheets.
10.4  Molecular Editor
10.5  Chemical Search
10.6  2D Ligand Interaction Diagram
10.7  Convert Chemicals to 3D
10.8  Generating Chemical Fragments
10.9  Find Bioisostere
10.10 Molcart
10.11 Calculate Properties
10.12 Standardize Table
10.13 Annotate By Substructure
10.14 Align/Color by 2D Scaffold
10.15 Set Formal Charges
10.16 Enumerate Formal Charge States
10.17 Convert
10.18 Build Prediction Model
10.19 Predict
10.20 Generate 3D Conformers
10.21 Generate Tautomers
10.22 Generate Stereoisomers
10.23 Prodrug
10.24 Ligand Energetics
10.25 Cluster Set
10.26 PCA Analysis
10.27 Visualize Chemical Space
10.28 Compare Two Sets
10.29 Merge Two Sets
10.30 Select Duplicates
10.31 Multi Parameter Optimization
10.32 Combinatorial Chemistry
10.33 SAR Analysis
10.34 Substructure Superposition
10.35 Atomic Property Field Superposition
10.36 APF Tools
11 Learn and Predict
11.1 Learn
11.2 Predict
11.3 Fingerprint Methods
11.4 3D QSAR
11.5 A Little Theory on Learning
12 Docking
12.1 Small Molecule Docking
12.2 Induced Fit (Flexible) Docking
12.3 Template Docking
12.4 Covalent Docking
12.5 De Novo Tools
12.6 ICM X-Ray AutoFit - Automated Model Building into Density
12.7 Protein-Protein Docking
13 Virtual Ligand Screening
13.1 Virtual Ligand Screening
13.2 Fragment Screening
13.3 Ligand-Based Screening using APF 3D Pharmacophores
14 MolScreen
14.1 Model Types
14.2 Brief Panel
14.3 Full Model Panel
14.4 Custom Model Panel
14.5 Results Table
14.6 Make Chemical Classification Model
14.7 Make APF Docking SAR Model
14.8 Predict Metabolic Oxidation
15 The 3D Fully Interactive Ligand Editor
15.1  Setup Ligand and Receptor
15.2  Ligand-Editor-Preferences
15.3  Display Options
15.4  Evaluate Ligand Score and Strain
15.5  Edit Ligand
15.6  Virtual Screen: Find Best Replacement Group
15.7  Multiple Position Group Scan
15.8  Bioisostere Scan
15.9  Dock or Minimize Ligand
15.10 Dock from Table
15.11 Fragment Linking
15.12 Impose Tethers or Distance Restraints
15.13 Docking Templates
15.14 Defined Flexible Receptor Groups
15.15 Side Chain Refinement
15.16 Multiple Receptor Docking
15.17 Covalent Docking in the Ligand Editor
15.18 Dock to Atomic Property Fields
15.19 How to Save Ligand Receptor Complex as PDB
15.20 Export Docking Project.
15.21 Close and Clean Up Project
16 Working with Tables and Plots
16.1 Standard ICM Tables
16.2 Molecular Tables
16.3 Insert Interactive Objects into Table Cell
16.4 Plotting Table Data
16.5 Principal Component Analysis
16.6 Learn and Predict
16.7 Data Clustering
17 Working with Local Databases
17.1 How to make a local database.
17.2 Browse Database
17.3 Edit Database
17.4 Query Local Database
18 ICM-Scarab - Data Capture, Integrator and Miner
18.1 Scrab Installation
18.2 Upload Data
18.3 Query Metadata
18.4 Browse and Export Data
18.5 Add a New User
18.6 Create a New Project and Assign User
18.7 Pages
19 ICM in KNIME
20 Tutorials
20.1  Graphics Tutorials
20.2  Creating Fully Interactive Slides for PowerPoint and the Web Tutorial
20.3  Protein Structure Tutorials
20.4  Sequence and Alignment Tutorials
20.5  Protein Modeling Tutorials
20.6  Cheminformatics Tutorials
20.7  3D Ligand Editor Tutorial
20.8  Atomic Property Field Tutorials
20.9  Ligand Docking Tutorials
20.10 Protein-Protein Docking Tutorial using FFT Method
20.11 Virtual Ligand Screening Tutorials
20.12 Induced Fit (Flexibility) Docking Tutorials
20.13 Chemical FingerPrint QSAR Model Tutorial
20.14 3D QSAR Tutorial
21 Frequently Asked Questions
21.1  FAQ Installation and Troubleshooting
21.2  FAQ Graphics and Display
21.3  FAQ ActiveICM
21.4  FAQ Structure
21.5  FAQ-Docking
21.6  FAQ-Sequences and Alignments
21.7  FAQ-Modeling
21.8  FAQ-Cheminformatics
21.9  FAQ-MolCart
21.10 FAQ-Script

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