MetaSite user manual
Gabriele Cruciani
Riccardo Vianello
Ismael Zamora
Edited by
Gianluca Sforna
Paolo Benedetti
Copyright © 2002, 2006 Molecular Discovery Ltd.
- Table of Contents
- 1. Overview
- 1.1. What is MetaSite?
- 1.2. MetaSite features
- 1.3. What MetaSite is not?
- 1.4. Program citation.
- 1.5. Program organization
- 1.6. Limitations.
- 1.7. User's support.
- 2. Background
- 3. Installation
- 4. Command line options
- 4.1. Examples
- 5. MetaSite menu bars
- 5.1. File menu
- 5.1.1. Open/Open ascii
- 5.1.2. Close
- 5.1.3. Save
- 5.1.4. Save As/Save_As_Ascii
- 5.1.5. Export As SD File
- 5.1.6. Exit
- 5.2. MetaSite menu
- 5.2.1. Sketch substrate
- 5.2.2. Load substrates as single conformers
- 5.2.3. Load substrates as conformer sets
- 5.2.4. Enter SMILES string
- 5.2.5. Load SMILES list
- 5.2.6. Run site of metabolism prediction
- 5.2.7. Evaluate inhibition
- 5.2.8. Tabulate
- 5.3. View menu
- 5.3.1. 2D View
- 5.3.2. Substrate rendering
- 5.3.3. Atoms color
- 5.3.4. Sort histograms
- 5.3.5. Reactivity correction
- 5.3.6. Tool bar
- 5.3.7. Status bar
- 5.3.8. Interface Style
- 5.4. CYP menu
- 5.4.1. Import enzyme
- 5.5. Help menu
- 6. MetaSite tutorial
- 6.1. Case study 1. Direct editing of substrate structures.
- 6.2. Case study 2. Input of Salmeterol as single conformation file.
- 6.3. Case study 3. Comparing common reactivity criteria and metabolic reactivity.
- 6.4. Case study 4. Prediction results using different cytochrome models on the same substrates structures.
- 6.5. Case study 5. MetaSite applications.
- 6.6. Case study 6. Running MetaSite from the command line
- 6.7. Conclusions
- A. Sketching small molecules
- A.1. Get starting
- A.2. Atom types
- A.3. 3D converting procedure
- A.4. Toolbar items and controls
- A.4.1. Clear document
- A.4.2. Undo/Redo
- A.4.3. Change atom type
- A.4.4. Insert bond
- A.4.5. Increase/Decrease charge
- A.4.6. Select
- A.4.7. Move
- A.4.8. Rotate
- A.4.9. Delete
- A.4.10. Group/Ungroup
- A.4.11. Select all
- A.4.12. Show atom colors
- A.4.13. Show warnings
- A.4.14. Show explicit hydrogens
- A.4.15. Implicit hydrogens
- A.4.16. Zoom
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