- Table of Contents
- 1. Overview
- 1.1. Manual organization
- 1.2. Citing MoKa
- 2. Installation
- 3. Background
- 4. MoKa graphical user interface (GUI)
- 4.1. The Menus
- 4.2. Working with MoKa
- 4.2.1. Importing Your Data
- 4.2.2. MoKa pKa predictions
- 4.2.3. Tautomers
- 4.2.4. The Graph
- 4.2.5. Exporting Your Results: batch calculation and snapshot
- 4.2.6. Custom models
- 4.3. Technical info
- 5. MoKa command-line
- 5.1. Output format
- 5.1.1. Plain text (txt) format
- 5.1.2. SD file format
- 6. Kibitzer: Extend pKa accuracy
- 6.1. The Interface and the Workflow
- 6.2. The Menus
- 6.3. Working with Kibitzer
- 6.3.1. Step 1: Import SD file
- 6.3.2. Step 2: Check assigned pKas
- 6.3.3. Step 3: Build Models
- 6.4. Tips and Troubleshooting
- 6.5. Capabilities and Limitations
- 7. Blabber: Generate Protomers
- 7.1. Blabber workflow
- 7.2. Command-line options
- 7.2.1. Basic usage examples
- 7.2.2. Advanced usage examples
- 7.3. Output format
- 8. Tauthor: Generate Tautomers
- 9. Versus
- 9.1. The Interface
- 9.2. The Menus
- 9.3. Working with Versus
- Colophon
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