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
*[[Testset Protocols]]
+
*[[Benchmarking Protocols and Results]]  
*[[Scoring Functions]]
+
** testset, pose reproduction, crossdocking, database enrichment SOP and other algorithm results
*[[Sampling Methods]]
+
*[[Additional DOCK6 Information]]
*[[Analog Library - Pubchem & Zinc]]
+
** miscellaneous information for DOCK scoring functions and experiments (some legacy)
*[[ZINC12 Database]]
 
*[[ZINC15 Database]]
 
*[[DOCK Installation]]
 
*[[Optimize Polar Hydrogens]]
 
*[[Virtual Screening Protocol]]
 
*[[Footprint Plot Visualization]]
 
*[[Sphere Generation]]
 
*[[Release]]
 
 
|}
 
|}
  
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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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*[[valgrind]]
 
*[[valgrind]]
 
*[[Ghostscript]]
 
*[[Ghostscript]]
|}
 
 
== De novo Design using DOCK ==
 
{| cellpadding=0 width=90%
 
*[[De Novo Design (DOCK_DN)]]
 
*[[Small Molecule Evolution (DOCK_GA)]]
 
 
|}
 
|}
  
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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)]
*[http://blaster.docking.org/zinc/ ZINC (ligand database)]
+
*[[ZINC12 Database]]
 +
*[[ZINC15 Database]]
 
*[[Families in the Protein Databank]]
 
*[[Families in the Protein Databank]]
 
*[[Automated Family generation from PDB]]
 
*[[Automated Family generation from PDB]]
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* [[pdb to mol2]]
 
* [[pdb to mol2]]
 
* [[SDF to mol2]]
 
* [[SDF to mol2]]
 
== Setting up accounts ==
 
{| cellpadding=0 width=90%
 
*[[Getting a BNL Account]]
 
*[[Activating your Seawulf Account]]
 
*[[Rotation students Wiki]]
 
*[[Setting up RSA SecureID token]]
 
|}
 
 
== Miscellaneous ==
 
{| cellpadding=0 width=90%
 
*[[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