Difference between revisions of "Rizzo Lab Information and Tutorials"

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{| 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]]  
*[[Benchmarking]]
+
** virtual screen, de novo design, genetic algorithm, covalent
*[[Developer's Info]]
+
*[[Benchmarking Protocols and Results]]  
*[[Testset Protocols]]
+
** testset, pose reproduction, crossdocking, database enrichment SOP and other algorithm results
*[[Parameter List/Explanations]]
+
*[[Additional DOCK6 Information]]
*[[Scoring Functions]]
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** miscellaneous information for DOCK scoring functions and experiments (some legacy)
*[[Example Input Files]]
 
*[[DOCK Abbreviations Guide]]
 
*[[Advanced Dock Utilities/Information]]
 
*[[DOCK6 POSE Reproduction]]
 
*[[Virtual Screening SOP]]
 
 
|}
 
|}
  
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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]]
 
== Setting up accounts ==
 
{| cellpadding=0 width=90%
 
*[[Activating your Seawulf Account]]
 
*[[Rotation students Wiki]]
 
|}
 
 
 
 
== Miscellaneous ==
 
{| cellpadding=0 width=90%
 
* [[How to purchase compounds for Rizzo lab]]
 
* [[X-Win32]]
 
* [[CVS Commands]]
 
* [[Ethernet Cables]]
 
* [[Sequence alignment]]
 
* [[Making images for publication]]
 
* [[Lab-designed code and programs]]
 
* [[Server Administration]]
 
* [[Amber on Seawulf (compilation)]]
 
* [[Cluster compilations]]
 
* [[NAMD on Seawulf]]
 
* [[Semester Checklist]]
 
* [[Wiki Editing]]
 
*[[Other Meetings]]
 
*[[Seawulf Cluster Assessment]]
 
*[[Formatting your Thesis]]
 
*[[Setting up insurance through Research Foundation]]
 
|}
 
 
==Archive==
 
*[[Legacy Info]]
 

Latest revision as of 10:50, 25 March 2024

DOCK

Visualization Software

Basic Linux Tools

Molecular Dynamics

GROMACS

Monte Carlo

Analysis Tools

Databases

Conversion between file types