Table of contents 1 Introduction 2 Help Videos on YouTube 3 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 4 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 5 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 5.8 Scan Pockets by 3D Pharmacophore 6 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 7 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) 8 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 9 Protein Modeling 9.1 Homology Modeling 9.2 Residue Renumber 9.3 Loop Modeling 9.4 Design Loop 9.5 Graft Loop 9.6 Loop Preferred Residues 9.7 Find Loops in PDB 9.8 Regularization 9.9 Refine Side Chains 9.10 Making a disulfide bond. 9.11 Making a Mutation 9.12 Modify Amino Acid 9.13 Predicting Change in Binding Free Energy upon Mutation 9.14 Predicting Change in Protein Stability upon Mutation 9.15 Effect of Mutation on Protein-Peptide 9.16 Effect of Mutation on Protein Ligand Binding 9.17 Predict Disulfide Bond 9.18 Protein Sculpting 9.19 Sample Protein 9.20 Sample Peptide 9.21 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 Torsion Analysis 10.17 Calculate Torsion Free Strain 10.18 Enumerate Formal Charge States 10.19 Protonation States vs pH 10.20 Convert 10.21 Build Prediction Model 10.22 Predict 10.23 Generate 3D Conformers 10.24 Generate Tautomers 10.25 Generate Stereoisomers 10.26 Prodrug 10.27 Ligand Energetics 10.28 Cluster Set 10.29 PCA Analysis 10.30 Visualize Chemical Space 10.31 Compare Two Sets 10.32 Merge Two Sets 10.33 Select Duplicates 10.34 Multi Parameter Optimization 10.35 Combinatorial Chemistry 10.36 SAR Analysis 10.37 Chemical Superposition 10.38 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 Docking: Introduction and Best Practices 12.2 Docking Steps 12.3 Run the Docking Simulation 12.4 Display & Analyze Docking Results 12.5 Interaction Restraints 12.6 Induced Fit (Flexible) Docking 12.7 Template Docking 12.8 Covalent Docking 12.9 Hybridize Chimeric Ligands 12.10 Ligand AIDE: AI Design Evolution 12.11 ICM X-Ray AutoFit - Automated Model Building into Density 12.12 Peptide Docking 12.13 Protein-Protein Docking 12.14 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 13.5 RIDGE - Rapid Docking GPU Engine 14 Molecular Dynamics 14.1 Run Molecular Dynamics 14.2 Restraints 14.3 Membrane 14.4 MD of VLS Hitlist 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 Defined Flexible Receptor Groups 16.14 Side Chain Refinement 16.15 Multiple Receptor Docking 16.16 Covalent Docking in the Ligand Editor 16.17 Dock to Atomic Property Fields 16.18 AI Decoration (groupGen) 16.19 How to Save Ligand Receptor Complex as PDB 16.20 Peptide Modeling 16.21 Export Docking Project. 16.22 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 18.5 Eficient Storage for Ultra-Large Virtual Chemical Databases 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