- Table of Contents
- 1. Background
- 1.1. The MoKa manual
- 1.2. pKa overview
- 1.3. MoKa pKa prediction method
- 1.4. Multiple ionization sites
- 1.5. Tautomeric forms
- 1.6. Covalent hydration
- 1.7. Citing MoKa
- 2. MoKa graphical user interface (GUI)
- 2.1. The Menus
- 2.2. Working with MoKa
- 2.2.1. Importing Your Data
- 2.2.2. MoKa pKa predictions
- 2.2.3. Tautomers
- 2.2.4. The Graph
- 2.2.5. Exporting Your Results: batch calculation and snapshot
- 2.2.6. Custom models
- 2.3. Technical info
- 3. MoKa command line
- 3.1. Output format
- 4. Kibitzer: Extend pKa accuracy
- 4.1. The Interface and the Workflow
- 4.2. The Menus
- 4.3. Working with Kibitzer
- 4.3.1. Step 1: Import SD file
- 4.3.2. Step 2: Check assigned pKas
- 4.3.3. Step 3: Build Models
- 4.4. Tips and Troubleshooting
- 4.5. Capabilities and Limitations
- 5. Blabber: Generate Protomers
- 5.1. Blabber workflow
- 5.2. Command line options
- 5.2.1. Basic usage examples
- 5.2.2. Advanced usage examples
- 6. Tauthor: Generate Tautomers
- 7. Versus
- 7.1. The Interface
- 7.2. The Menus
- 7.3. Working with Versus
- Colophon
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