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Table of contents
Data flow in Lead-Finder ........................................................................ 3
Protein Structure And Its Preparation For Docking ..................................... 4
Ligand Structure And Its Preparation For Docking ...................................... 5
Installation ........................................................................................... 6
Configuration Options for Docking ........................................................... 8
Command Line Options ........................................................................ 11
Example 1: Calculating energy grid maps. ........................................... 12
Example 1: Calculating energy grid maps. ........................................... 12
Example 2: Calculating free energy of binding. ..................................... 13
Example 3: Ligand docking with pre-calculated grid maps. ..................... 13
Example 4: Virtual screening. ............................................................ 14
Example 5: Preparation of trypsin structure for docking. ........................ 15
Example 6: Preparation of progesterone structure for docking. ............... 16
Example 7: Preparation of methanol dehydrogenase structure for docking.
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Example 8: Docking to cytochrome p450. ............................................ 18
Glossary ......................................................................................... 19
Lead-Finder v.1.1.10 User Manual