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
 +
*[[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]]
+
*[[Unix]]
|[[vi ]]
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*[[vi ]]
|[[sed - Stream Editor in Unix]]
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*[[sed - Stream Editor in Unix]]
|-
+
*[[Slick awk tricks]]
|[[Stupid awk tricks]]
+
*[[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]]
+
*[[C Shell Scripting]]
|[[C Shell Scripting]]
+
*[[Unix find]]
|-
+
*[[Which Unix Distribution?]]
|[[Unix find]]
+
*[[rsync]]
|[[Which Unix Distribution?]]
+
*[[MPICH]]
|[[rsync]]
+
*[[Secure Shell (ssh)]]
|-
+
*[[Archiving old data]]
|[[MPICH]]
+
*[[valgrind]]
|[[Secure Shell (ssh)]]
+
*[[Ghostscript]]
|[[Archiving old data]]
 
|-
 
|[[valgrind]]
 
|[[Ghostscript]]
 
|}
 
 
 
== Docking ==
 
{| cellpadding=0 width=90%
 
|[[DOCK Tutorials]]
 
|[[Testset Protocols]]
 
|[[Scoring Functions]]
 
|[[Sampling Methods]]
 
|-
 
|[[ZINC12 Database]]
 
|[[ZINC15 Database]]
 
|[[Installing DOCK]]
 
|[[Optimize Polar Hydrogens]]
 
|[[Virtual Screening Protocol]]
 
|-
 
|[[Sphere Generation]]
 
|[[DOCK Compilation]]
 
|[[Virtual Screening Protocol on BlueGene (IGF-IR system)]]
 
|[[DOCK Benchmarking]]
 
|[[Release]]
 
|}
 
== De novo Design using DOCK ==
 
{| cellpadding=0 width=90%
 
|[[NOVA (Navigation and Optimization for Virtual Assembly]]
 
|[[CONGA]]
 
 
|}
 
|}
  
 
== Molecular Dynamics ==
 
== Molecular Dynamics ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
|[[AMBER Tutorials]]
+
*[[AMBER Tutorials]]
|[[AMBER TI Tutorials]]
+
*[[AMBER TI Tutorials]]
|[[AMBER Lipid Tutorials]]
+
*[[AMBER Lipid Tutorials]]
|[[AMBER tricks]]
+
*[[AMBER tricks]]
|-
+
*[[NAMD tutorial]]
|[[NAMD tutorial]]
+
*[[NAMD Amber inputs]]
|[[NAMD Amber inputs]]
+
*[[per-residue energy decompositions]]
|-
+
*[[nonstandard residues prep]]
|[[per-residue energy decompositions]]
+
*[[ptraj]]
|[[nonstandard residues prep]]
+
*[[Blocked Standard Error of the Mean]]
|-
 
|[[ptraj]]
 
|-
 
|[[Blocked Standard Error of the Mean]]
 
 
|}
 
|}
  
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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]]
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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 Families generation from the Protein Databank]]
+
*[[Automated Family generation from PDB]]
 
*[[Drug-like organic molecules]]
 
*[[Drug-like organic molecules]]
 
== BlueGene ==
 
{| cellpadding=0 width=90%
 
| [[Setup ssh tunnel to NYBlue fen]]
 
| [[Get time estimate for free blocks]]
 
| [[Get Job ids to use for llcancel]]
 
 
|-
 
| [[Submitting BlueGene Jobs]]
 
| [[Compiling Applications for BG/L]]
 
| [[LoadLeveler Chain Jobs]]
 
|-
 
| [[scp files from cluster to NYBlue]]
 
| [[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%
 
| [[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]]
 
|-
 
| [[Visiting BNL]]
 
| [[Making images for publication]]
 
| [[Lab-designed code and programs]]
 
| [[Server Administration]]
 
|-
 
| [[Amber on Seawulf (compilation)]]
 
| [[Cluster compilations]]
 
| [[NAMD on Seawulf]]
 
| [[Dell 5110cn Printer]]
 
|-
 
| [[Semester Checklist]]
 
| [[Wiki Editing]]
 
|-
 
|[[Stony Brook Joint Group Meetings in Computational Structural Biology]]
 
|[[Other Meetings]]
 
|[[Seawulf Cluster Assessment ]]
 
|}
 
 
== Formating Word Documents ==
 
 
[[Formating your Thesis]]
 
 
== 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