Download FITTED Suite 3.6 User Guide

FITTED Suite 3.5: User Guide
V.3. Parameters for the binding cavity file .......................................................................................... 22
V.4. Parameters for the Interaction Sites file ...................................................................................... 23
V.5. A simple ProCESS keyword file for rigid protein docking setup ................................................... 25
V.6. A simple ProCESS keyword file for flexible protein docking setup ............................................... 25
V.7. An advanced ProCESS keyword file ............................................................................................ 25
VI. Preparing a keyword file for SMART ............................................................................................... 26
VI.1. Input/output files ......................................................................................................................... 26
VI.2. Parameters for the preparation of the ligand file ........................................................................ 26
VI.3. A simple typical SMART keyword file .......................................................................................... 28
VI.4. An advanced typical SMART keyword file ................................................................................... 28
VII. Preparing a keyword file for FITTED .............................................................................................. 29
VII.1. Input/output files ........................................................................................................................ 29
VII.2. Run parameters ........................................................................................................................ 30
VII.3. Conjugate gradient parameters ................................................................................................ 31
VII.4. Energy parameters ................................................................................................................... 32
VII.5. Scoring parameters ................................................................................................................... 34
VII.6. Initial population parameters ..................................................................................................... 34
VII.7. Evolution parameters ................................................................................................................ 35
VII.8. Docking of covalent inhibitors ................................................................................................... 37
VII.9. Output/convergence parameters .............................................................................................. 38
VII.10. A simple FITTED keyword file for rigid protein docking ............................................................ 39
VII.11. A simple FITTED keyword file for flexible protein docking........................................................ 39
VII.12. A template FITTED keyword file with all the possible keywords .............................................. 39
VIII. Analysis of a docking run with FITTED ........................................................................................ 42
VIII.1. The log file................................................................................................................................ 42
VIII.2. The output file .......................................................................................................................... 43
VIII.3. The results file .......................................................................................................................... 43
VIII.4. The ligand mol2 file .................................................................................................................. 43
VIII.5. The sdf file................................................................................................................................ 43
VIII.6. The protein mol2 file (flexible protein mode only) .................................................................... 44
VIII.7. The protein pdb file (flexible protein mode only) ...................................................................... 44
Appendix A: FITTED Input File Formats............................................................................................... 45
A.1. The protein files ....................................................................................................................... 46
A.1.1. The XXXX_dock.mol2 .......................................................................................................... 46
A.1.2. The XXXX_score.mol2 file ................................................................................................... 46
A.1.3. The XXXX_site.txt file ........................................................................................................... 48
A.2. The Ligand file ......................................................................................................................... 48
3