Difference between revisions of "Rizzo Lab Information and Tutorials"

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== DOCK ==
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{| cellpadding=0 width=90%
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*[http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm Online Users Manual]
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*[[Tutorials]]
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*[[Benchmarking]]
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*[[Developer's Info]]
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*[[Testset Protocols]]
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*[[Parameter List/Explanations]]
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*[[Scoring Functions]]
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*[[Example Input Files]]
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*[[DOCK Abbreviations Guide]]
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*[[Advanced Dock Utilities/Information]]
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*[[DOCK6 POSE Reproduction]]
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|}
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== Visualization Software ==
 
== Visualization Software ==
 
*[[Chimera]]
 
*[[Chimera]]
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*[[valgrind]]
 
*[[valgrind]]
 
*[[Ghostscript]]
 
*[[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]]
 
*[[Footprint Plot Visualization]]
 
*[[Sphere Generation]]
 
*[[DOCK Compilation]]
 
*[[Virtual Screening Protocol on BlueGene (IGF-IR system)]]
 
*[[DOCK Benchmarking]]
 
*[[Release]]
 
|}
 
 
== 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 ==
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* [[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)]
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*[[ZINC12 Database]]
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*[[ZINC15 Database]]
 
*[[Families in the Protein Databank]]
 
*[[Families in the Protein Databank]]
*[[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 ==
 
{| 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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== Setting up accounts ==
 
== Setting up accounts ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
| [[Getting a BNL Account]]
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*[[Activating your Seawulf Account]]
| [[Activating your Seawulf Account]]
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*[[Rotation students Wiki]]
| [[Rotation students Wiki]]
 
| [[Setting up RSA SecureID token]]
 
 
|}
 
|}
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 +
== AutoDock4 ==
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{|
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*[[AutoDock4 Pose Reproduction Tutorial]]
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*[[AutoDock4 Crossdock]]
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*[[AutoDock4 Benchmark Results]]
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|}
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== AutoDock Vina ==
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{|
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*[[AutoDock Vina Pose Reproduction Tutorial]]
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*[[AutoDock Vina Benchmark Results]]
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|}
  
 
== Miscellaneous ==
 
== Miscellaneous ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
| [[X-Win32]]  
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* [[How to write Makefiles]]
| [[CVS Commands]]
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* [[X-Win32]]  
| [[Ethernet Cables]]
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* [[CVS Commands]]
| [[Sequence alignment]]  
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* [[Ethernet Cables]]
|-
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* [[Sequence alignment]]  
| [[Visiting BNL]]
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* [[Making images for publication]]
| [[Making images for publication]]
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* [[Lab-designed code and programs]]
| [[Lab-designed code and programs]]
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* [[Server Administration]]
| [[Server Administration]]
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* [[Amber on Seawulf (compilation)]]
|-
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* [[Cluster compilations]]
| [[Amber on Seawulf (compilation)]]
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* [[NAMD on Seawulf]]
| [[Cluster compilations]]
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* [[Semester Checklist]]
| [[NAMD on Seawulf]]
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* [[Wiki Editing]]
| [[Dell 5110cn Printer]]
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*[[Other Meetings]]
|-
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*[[Seawulf Cluster Assessment]]
| [[Semester Checklist]]
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*[[Formatting your Thesis]]
| [[Wiki Editing]]
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*[[Setting up insurance through Research Foundation]]
|-
 
|[[Stony Brook Joint Group Meetings in Computational Structural Biology]]
 
|[[Other Meetings]]
 
|[[Seawulf Cluster Assessment ]]
 
 
|}
 
|}
 
== Formating Word Documents ==
 
 
[[Formating your Thesis]]
 
 
== Insurance ==
 
[[Research Foundation]]
 
  
 
==Archive==
 
==Archive==
[[Legacy Info]]
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*[[Legacy Info]]

Latest revision as of 10:27, 15 September 2020

DOCK

Visualization Software

Basic Linux Tools

Molecular Dynamics

GROMACS

Monte Carlo

Analysis Tools

Databases

Conversion between file types

Setting up accounts

AutoDock4

AutoDock Vina

Miscellaneous

Archive