Difference between revisions of "Rizzo Lab Information and Tutorials"
From Rizzo_Lab
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*[http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm Online Users Manual] | *[http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm Online Users Manual] | ||
| − | *[[Tutorials]] | + | *[[Tutorials]] |
| − | * | + | ** virtual screen, de novo design, genetic algorithm, covalent |
| − | * | + | *[[Benchmarking Protocols and Results]] |
| − | *[[ | + | ** testset, pose reproduction, crossdocking, database enrichment SOP and other algorithm results |
| − | * | + | *[[Additional DOCK6 Information]] |
| − | * | + | ** miscellaneous information for DOCK scoring functions and experiments (some legacy) |
| − | *[[ | ||
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| − | * | ||
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*[[Ways to remove the first line]] | *[[Ways to remove the first line]] | ||
*[[PBS Queue]] | *[[PBS Queue]] | ||
| + | *[[Useful Slurm Commands]] | ||
*[[gdb (GNU Debugger)]] | *[[gdb (GNU Debugger)]] | ||
*[[Common Errors - ctrl M]] | *[[Common Errors - ctrl M]] | ||
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* [[pdb to mol2]] | * [[pdb to mol2]] | ||
* [[SDF to mol2]] | * [[SDF to mol2]] | ||
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Latest revision as of 10:50, 25 March 2024
Contents
DOCK
Visualization Software
Basic Linux Tools
Molecular Dynamics
GROMACS
Monte Carlo
Analysis Tools
Databases
- PubChem (ligand database)
- NIST (small molecule database)
- ZINC12 Database
- ZINC15 Database
- Families in the Protein Databank
- Automated Family generation from PDB
- Drug-like organic molecules
