Nov 28 2022 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
Molecular Dynamics
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index
#set title ICM User's Guide

ICM-Pro User Guide v.3.9

by Ruben Abagyan, Andrew Orry, Eugene Raush, and Maxim Totrov
Copyright © 2022



Nov 28 2022

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
5.7 3D Similarity PDB Search
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 Protonation States vs pH
10.18 Convert
10.19 Build Prediction Model
10.20 Predict
10.21 Generate 3D Conformers
10.22 Generate Tautomers
10.23 Generate Stereoisomers
10.24 Prodrug
10.25 Ligand Energetics
10.26 Cluster Set
10.27 PCA Analysis
10.28 Visualize Chemical Space
10.29 Compare Two Sets
10.30 Merge Two Sets
10.31 Select Duplicates
10.32 Multi Parameter Optimization
10.33 Combinatorial Chemistry
10.34 SAR Analysis
10.35 Substructure Superposition
10.36 Atomic Property Field Superposition
10.37 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 ICM X-Ray AutoFit - Automated Model Building into Density
12.6 Peptide Docking
12.7 Protein-Protein Docking
12.8 PROTAC Modeling
13 Virtual Ligand Screening
13.1 Virtual Ligand Screening
13.2 Fragment Screening
13.3 Ligand-Based Screening using APF 3D Pharmacophores
13.4 RIDE Rapid Isostere Discovery Engine
14 Molecular Dynamics
15 MolScreen
15.1 Load Models and Run MolScreen
15.2 Results Table
15.3 Model Types
15.4 Custom Model Panel
15.5 Make Chemical Classification Model
15.6 Make APF Docking SAR Model
15.7 Predict Metabolic Oxidation
16 The 3D Fully Interactive Ligand Editor
16.1  Setup Ligand and Receptor
16.2  Ligand-Editor-Preferences
16.3  Display Options
16.4  Evaluate Ligand Score and Strain
16.5  Edit Ligand
16.6  Virtual Screen: Find Best Replacement Group
16.7  Multiple Position Group Scan
16.8  Bioisostere Scan
16.9  Dock or Minimize Ligand
16.10 Dock from Table
16.11 Fragment Linking Core Replacement
16.12 Impose Tethers or Distance Restraints
16.13 Docking Templates
16.14 Defined Flexible Receptor Groups
16.15 Side Chain Refinement
16.16 Multiple Receptor Docking
16.17 Covalent Docking in the Ligand Editor
16.18 Dock to Atomic Property Fields
16.19 How to Save Ligand Receptor Complex as PDB
16.20 Export Docking Project.
16.21 Close and Clean Up Project
17 Working with Tables and Plots
17.1 Standard ICM Tables
17.2 Molecular Tables
17.3 Insert Interactive Objects into Table Cell
17.4 Plotting Table Data
17.5 Principal Component Analysis
17.6 Learn and Predict
17.7 Data Clustering
18 Working with Local Databases
18.1 How to make a local database.
18.2 Browse Database
18.3 Edit Database
18.4 Query Local Database
19 ICM-Scarab - Data Capture, Integrator and Miner
19.1 Scrab Installation
19.2 Upload Data
19.3 Query Metadata
19.4 Browse and Export Data
19.5 Add a New User
19.6 Create a New Project and Assign User
19.7 Pages
20 ICM in KNIME
21 Tutorials
21.1  Graphics Tutorials
21.2  Creating Fully Interactive Slides for PowerPoint and the Web Tutorial
21.3  Protein Structure Tutorials
21.4  Sequence and Alignment Tutorials
21.5  Protein Modeling Tutorials
21.6  Cheminformatics Tutorials
21.7  3D Ligand Editor Tutorial
21.8  Atomic Property Field Tutorials
21.9  Ligand Docking Tutorials
21.10 Protein-Protein Docking Tutorial using FFT Method
21.11 Virtual Ligand Screening Tutorials
21.12 Induced Fit (Flexibility) Docking Tutorials
21.13 Chemical FingerPrint QSAR Model Tutorial
21.14 3D QSAR Tutorial
22 Frequently Asked Questions
22.1  FAQ Installation and Troubleshooting
22.2  FAQ Graphics and Display
22.3  FAQ ActiveICM
22.4  FAQ Structure
22.5  FAQ-Docking
22.6  FAQ-Sequences and Alignments
22.7  FAQ-Modeling
22.8  FAQ-Cheminformatics
22.9  FAQ-MolCart
22.10 FAQ-Script

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