Difference between revisions of "Rizzo Lab Information and Tutorials"
From Rizzo_Lab
(→Setting up accounts) |
(→DOCK) |
||
| (95 intermediate revisions by 8 users not shown) | |||
| Line 1: | Line 1: | ||
| + | == DOCK == | ||
| + | {| cellpadding=0 width=90% | ||
| + | *[http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm 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 == | == Visualization Software == | ||
*[[Chimera]] | *[[Chimera]] | ||
| Line 12: | 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 23: | Line 35: | ||
*[[valgrind]] | *[[valgrind]] | ||
*[[Ghostscript]] | *[[Ghostscript]] | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
|} | |} | ||
| Line 76: | Line 61: | ||
== Analysis Tools == | == Analysis Tools == | ||
| + | * [[Analysis Tools Repository]] | ||
* [[MATLAB]] | * [[MATLAB]] | ||
* [[Octave]] | * [[Octave]] | ||
| Line 85: | Line 71: | ||
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem (ligand database)] | *[http://pubchem.ncbi.nlm.nih.gov/ PubChem (ligand database)] | ||
*[http://webbook.nist.gov/chemistry/ NIST (small molecule database)] | *[http://webbook.nist.gov/chemistry/ NIST (small molecule database)] | ||
| − | *[ | + | *[[ZINC12 Database]] |
| + | *[[ZINC15 Database]] | ||
*[[Families in the Protein Databank]] | *[[Families in the Protein Databank]] | ||
| − | *[[Automated | + | *[[Automated Family generation from PDB]] |
*[[Drug-like organic molecules]] | *[[Drug-like organic molecules]] | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
== Conversion between file types == | == Conversion between file types == | ||
| Line 108: | Line 83: | ||
* [[pdb to mol2]] | * [[pdb to mol2]] | ||
* [[SDF to mol2]] | * [[SDF to mol2]] | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
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
