Difference between revisions of "Rizzo Lab Information and Tutorials"
From Rizzo_Lab
Stonybrook (talk | contribs) |
(→DOCK) |
||
| (44 intermediate revisions by 6 users not shown) | |||
| Line 2: | Line 2: | ||
{| cellpadding=0 width=90% | {| cellpadding=0 width=90% | ||
*[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) |
| − | *[[ | ||
| − | |||
| − | |||
| − | * | ||
| − | * | ||
|} | |} | ||
| Line 28: | Line 23: | ||
*[[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]] | ||
| Line 87: | Line 83: | ||
* [[pdb to mol2]] | * [[pdb to mol2]] | ||
* [[SDF to mol2]] | * [[SDF to mol2]] | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
Latest revision as of 11:50, 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
