Difference between revisions of "Rizzo Lab Information and Tutorials"
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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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* [[pdb to mol2]] | * [[pdb to mol2]] | ||
* [[SDF to mol2]] | * [[SDF to mol2]] | ||
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Latest revision as of 11:50, 25 March 2024
Contents
[hide]DOCK
- Online Users Manual
- 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)
Visualization Software
Basic Linux Tools
- Unix
- vi
- sed - Stream Editor in Unix
- Slick awk tricks
- Ways to remove the first line
- PBS Queue
- Useful Slurm Commands
- gdb (GNU Debugger)
- Common Errors - ctrl M
- C Shell Scripting
- Unix find
- Which Unix Distribution?
- rsync
- MPICH
- Secure Shell (ssh)
- Archiving old data
- valgrind
- Ghostscript
Molecular Dynamics
- AMBER Tutorials
- AMBER TI Tutorials
- AMBER Lipid Tutorials
- AMBER tricks
- NAMD tutorial
- NAMD Amber inputs
- per-residue energy decompositions
- nonstandard residues prep
- ptraj
- Blocked Standard Error of the Mean
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
