Difference between revisions of "Rizzo Lab Information and Tutorials"
From Rizzo_Lab
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| + | == DOCK == | ||
| + | {| cellpadding=0 width=90% | ||
| + | *[http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm Online Users Manual] | ||
| + | *[[Tutorials]] | ||
| + | *[[Benchmarking]] | ||
| + | *[[Developer's Info]] | ||
| + | *[[Testset Protocols]] | ||
| + | *[[Parameter List/Explanations]] | ||
| + | *[[Scoring Functions]] | ||
| + | *[[Example Input Files]] | ||
| + | *[[DOCK Abbreviations Guide]] | ||
| + | *[[Advanced Dock Utilities/Information]] | ||
| + | *[[DOCK6 POSE Reproduction]] | ||
| + | *[[Virtual Screening SOP]] | ||
| + | |} | ||
| + | |||
== Visualization Software == | == Visualization Software == | ||
*[[Chimera]] | *[[Chimera]] | ||
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*[[valgrind]] | *[[valgrind]] | ||
*[[Ghostscript]] | *[[Ghostscript]] | ||
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|} | |} | ||
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== Analysis Tools == | == Analysis Tools == | ||
| + | * [[Analysis Tools Repository]] | ||
* [[MATLAB]] | * [[MATLAB]] | ||
* [[Octave]] | * [[Octave]] | ||
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*[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]] | ||
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== Setting up accounts == | == Setting up accounts == | ||
{| cellpadding=0 width=90% | {| cellpadding=0 width=90% | ||
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*[[Activating your Seawulf Account]] | *[[Activating your Seawulf Account]] | ||
*[[Rotation students Wiki]] | *[[Rotation students Wiki]] | ||
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|} | |} | ||
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| + | == AutoDock4 == | ||
| + | {| | ||
| + | *[[AutoDock4 Pose Reproduction Tutorial]] | ||
| + | *[[AutoDock4 Crossdock]] | ||
| + | *[[AutoDock4 Benchmark Results]] | ||
| + | |} | ||
| + | |||
| + | == AutoDock Vina == | ||
| + | {| | ||
| + | *[[AutoDock Vina Pose Reproduction Tutorial]] | ||
| + | *[[AutoDock Vina Benchmark Results]] | ||
| + | |} | ||
== Miscellaneous == | == Miscellaneous == | ||
{| cellpadding=0 width=90% | {| cellpadding=0 width=90% | ||
| − | *[[X-Win32]] | + | * [[How to purchase compounds for Rizzo lab]] |
| + | * [[X-Win32]] | ||
* [[CVS Commands]] | * [[CVS Commands]] | ||
* [[Ethernet Cables]] | * [[Ethernet Cables]] | ||
* [[Sequence alignment]] | * [[Sequence alignment]] | ||
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* [[Making images for publication]] | * [[Making images for publication]] | ||
* [[Lab-designed code and programs]] | * [[Lab-designed code and programs]] | ||
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* [[Cluster compilations]] | * [[Cluster compilations]] | ||
* [[NAMD on Seawulf]] | * [[NAMD on Seawulf]] | ||
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* [[Semester Checklist]] | * [[Semester Checklist]] | ||
* [[Wiki Editing]] | * [[Wiki Editing]] | ||
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*[[Other Meetings]] | *[[Other Meetings]] | ||
*[[Seawulf Cluster Assessment]] | *[[Seawulf Cluster Assessment]] | ||
Latest revision as of 09:56, 16 June 2021
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
