Difference between revisions of "Rizzo Lab Information and Tutorials"

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(→‎De novo Design using DOCK)
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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]]
 +
** 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]]
−
|[[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]]
−
|[[Stupid awk tricks]]
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*[[Ways to remove the first line]]
−
|[[Ways to remove the first line]]
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*[[PBS Queue]]
−
|[[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]]
−
|[[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]]
−
|[[Which Unix Distribution?]]
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*[[MPICH]]
−
|[[rsync]]
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*[[Secure Shell (ssh)]]
−
|-
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*[[Archiving old data]]
−
|[[MPICH]]
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*[[valgrind]]
−
|[[Secure Shell (ssh)]]
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*[[Ghostscript]]
−
|[[Archiving old data]]
 
−
|-
 
−
|[[valgrind]]
 
−
|[[Ghostscript]]
 
−
|}
 
−
 
 
−
== Docking ==
 
−
{| cellpadding=0 width=90%
 
−
|[[DOCK Tutorials]]
 
−
|[[Covalent DOCK]]
 
−
|[[Testset Protocols]]
 
−
|[[Scoring Functions]]
 
−
|[[Sampling Methods]]
 
−
|[[3D Analog Library Generation Using Pubchem and Zinc]]
 
−
|-
 
−
|[[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 (CONstruction by Genetic Algorithm)]]
 
 
|}
 
|}
  
 
== 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 Lipid Tutorials]]
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*[[AMBER Lipid Tutorials]]
−
|[[AMBER tricks]]
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*[[AMBER tricks]]
−
|-
+
*[[NAMD tutorial]]
−
|[[NAMD tutorial]]
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*[[NAMD Amber inputs]]
−
|[[NAMD Amber inputs]]
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*[[per-residue energy decompositions]]
−
|-
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*[[nonstandard residues prep]]
−
|[[per-residue energy decompositions]]
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*[[ptraj]]
−
|[[nonstandard residues prep]]
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*[[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

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