Difference between revisions of "Rizzo Lab Information and Tutorials"

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== 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
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*[[Benchmarking Protocols and Results]]
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** 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]]
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== Basic Linux Tools==
 
== Basic Linux Tools==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
−
|[[Unix]]
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*[[Unix]]
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|[[vi ]]
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*[[vi ]]
−
|[[sed - Stream Editor in Unix]]
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*[[sed - Stream Editor in Unix]]
−
|-
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*[[Slick awk tricks]]
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|[[Stupid awk tricks]]
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*[[Ways to remove the first line]]
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|[[Ways to remove the first line]]
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*[[PBS Queue]]
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|[[PBS Queue]]
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*[[Useful Slurm Commands]]
−
|-
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*[[gdb (GNU Debugger)]]
−
|[[gdb (GNU Debugger)]]
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*[[Common Errors - ctrl M]]
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|[[Common Errors - ctrl M]]
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*[[C Shell Scripting]]
−
|[[C Shell Scripting]]
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*[[Unix find]]
−
|-
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*[[Which Unix Distribution?]]
−
|[[Unix find]]
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*[[rsync]]
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|[[Which Unix Distribution?]]
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*[[MPICH]]
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|[[rsync]]
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*[[Secure Shell (ssh)]]
−
|-
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*[[Archiving old data]]
−
|[[MPICH]]
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*[[valgrind]]
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|[[Secure Shell (ssh)]]
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*[[Ghostscript]]
−
|[[Archiving old data]]
 
−
|-
 
−
|[[valgrind]]
 
−
|[[Ghostscript]]
 
−
|}
 
−
 
 
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== Virtual Screening Protocol on BlueGene ==
 
−
Yulin Huang
 
−
In this document, the current Rizzo group protocol will be described in detail. This protocol has be through successive iterations and has be used to select compounds for Flu and HIVgp41 (number of purchased compounds for HIV = 112).
 
−
{| cellpadding=0 width=90%
 
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|[[DOCK Tutorials]]
 
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|[[Testset Protocols]]
 
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|[[Scoring Functions]]
 
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|[[Sampling Methods]]
 
−
|-
 
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|[[ZINC Database]]
 
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|[[Installing DOCK]]
 
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|[[Optimize Polar Hydrogens]]
 
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|[[Virtual Screening Protocol]]
 
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|-
 
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|[[Sphere Generation]]
 
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|[[DOCK Compilation]]
 
 
|}
 
|}
  
 
== Molecular Dynamics ==
 
== Molecular Dynamics ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
−
|[[AMBER Tutorials]]
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*[[AMBER Tutorials]]
−
|[[AMBER TI Tutorials]]
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*[[AMBER TI Tutorials]]
−
|[[AMBER tricks]]
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*[[AMBER Lipid Tutorials]]
−
|-
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*[[AMBER tricks]]
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|[[NAMD tutorial]]
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*[[NAMD tutorial]]
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|[[NAMD Amber inputs]]
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*[[NAMD Amber inputs]]
−
|-
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*[[per-residue energy decompositions]]
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|[[per-residue energy decompositions]]
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*[[nonstandard residues prep]]
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|[[nonstandard residues prep]]
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*[[ptraj]]
−
|-
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*[[Blocked Standard Error of the Mean]]
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|[[ptraj]]
 
 
|}
 
|}
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[http://www.ams.sunysb.edu/~tbalius/NamdandDockonNYBlue.pdf NAMD and DOCK on BlueGene ]
 
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===error analysis===
 
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[[Blocked Standard Error of the Mean]]
 
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[[autocorrelation function]]
 
  
 
== GROMACS ==
 
== GROMACS ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
−
|[[Compiling GROMACS on Cluster]]
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* [[Compiling GROMACS on Cluster]]
−
|-
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* [[MD Simulation: Protein in Water]]
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|[[MD Simulation: Protein in Water]]
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|}
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|[[MD Simulation: Protein-Ligand Complex]]
 
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|[[Membrane Protein Systems]]
 
−
|-
 
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|[[TI: Mutating Ligand to Nothing]]
 
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|[[TI: Mutating Ligand to Ligand]]
 
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|[[Steered MD / Umbrella Sampling]]
 
−
|-
 
−
|}
 
  
 
== Monte Carlo ==
 
== Monte Carlo ==
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== Analysis Tools ==
 
== Analysis Tools ==
 +
* [[Analysis Tools Repository]]
 
* [[MATLAB]]
 
* [[MATLAB]]
 
* [[Octave]]
 
* [[Octave]]
 
* [[R - Statistical Computing]]
 
* [[R - Statistical Computing]]
−
* [[Xmgrace]]
 
 
* [[gnuplot]]
 
* [[gnuplot]]
 
* [[pylab]]
 
* [[pylab]]
  
 
== Databases ==
 
== Databases ==
−
*[http://129.43.27.140/ncidb2/ NCI (ligand database)]
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*[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)]
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*[[ZINC12 Database]]
 +
*[[ZINC15 Database]]
 
*[[Families in the Protein Databank]]
 
*[[Families in the Protein Databank]]
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*[[Automated Families generation from the Protein Databank]]
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*[[Automated Family generation from PDB]]
 
*[[Drug-like organic molecules]]
 
*[[Drug-like organic molecules]]
−
 
−
== BlueGene ==
 
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{| cellpadding=0 width=90%
 
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| [[Setup ssh tunnel to NYBlue fen]]
 
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| [[Get time estimate for free blocks]]
 
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| [[Get Job ids to use for llcancel]]
 
−
 
−
|-
 
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| [[Submitting BlueGene Jobs]]
 
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| [[Compiling Applications for BG/L]]
 
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| [[LoadLeveler Chain Jobs]]
 
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|-
 
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| [[scp files from cluster to NYBlue]]
 
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| [[Get time for job completion]]
 
−
|}
 
  
 
== Conversion between file types ==
 
== Conversion between file types ==
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* [[pdb to mol2]]
 
* [[pdb to mol2]]
 
* [[SDF to mol2]]
 
* [[SDF to mol2]]
−
 
−
== Setting up accounts ==
 
−
{| cellpadding=0 width=90%
 
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| [[Getting a BNL Account]]
 
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| [[Activating your Seawulf Account]]
 
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| [[Rotation students Wiki]]
 
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| [[Setting up RSA SecureID token]]
 
−
|}
 
−
 
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== Miscellaneous ==
 
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{| cellpadding=0 width=90%
 
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| [[X-Win32]]
 
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| [[CVS Commands]]
 
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| [[Ethernet Cables]]
 
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| [[Sequence alignment]]
 
−
|-
 
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| [[Visiting BNL]]
 
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| [[Making images for publication]]
 
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| [[Lab-designed code and programs]]
 
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| [[Server Administration]]
 
−
|-
 
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| [[Amber on Seawulf (compilation)]]
 
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| [[Cluster compilations]]
 
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| [[NAMD on Seawulf]]
 
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| [[Dell 5110cn Printer]]
 
−
|-
 
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| [[Journal Articles from UCSF]]
 
−
| [[Semester Checklist]]
 
−
|}
 
−
 
−
== Insurance ==
 
−
[[Research Foundation]]
 

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

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