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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*[[Virtual Screening SOP]]
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|}
 +
 
== Visualization Software ==
 
== Visualization Software ==
 
*[[Chimera]]
 
*[[Chimera]]
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*[[valgrind]]
 
*[[valgrind]]
 
*[[Ghostscript]]
 
*[[Ghostscript]]
−
|}
 
−
 
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== Docking ==
 
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{| cellpadding=0 width=90%
 
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*[[DOCK Tutorials]]
 
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*[[Covalent DOCK]]
 
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*[[Testset Protocols]]
 
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*[[Scoring Functions]]
 
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*[[Sampling Methods]]
 
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*[[3D Analog Library Generation Using Pubchem and Zinc]]
 
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*[[ZINC12 Database]]
 
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*[[ZINC15 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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*[[Footprint Plot Visualization]]
 
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*[[Sphere Generation]]
 
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*[[DOCK Compilation]]
 
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*[[Virtual Screening Protocol on BlueGene (IGF-IR system)]]
 
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*[[DOCK Benchmarking]]
 
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*[[Release]]
 
−
|}
 
−
 
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== De novo Design using DOCK ==
 
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{| cellpadding=0 width=90%
 
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*[[De Novo Design (DOCK_DN)]]
 
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*[[Small Molecule Evolution (DOCK_GA)]]
 
 
|}
 
|}
  
 
== Molecular Dynamics ==
 
== Molecular Dynamics ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
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|[[AMBER Tutorials]]
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*[[AMBER Tutorials]]
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|[[AMBER TI Tutorials]]
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*[[AMBER TI Tutorials]]
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|[[AMBER Lipid Tutorials]]
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*[[AMBER Lipid Tutorials]]
−
|[[AMBER tricks]]
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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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*[[nonstandard residues prep]]
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|[[per-residue energy decompositions]]
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*[[ptraj]]
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|[[nonstandard residues prep]]
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*[[Blocked Standard Error of the Mean]]
−
|-
 
−
|[[ptraj]]
 
−
|-
 
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|[[Blocked Standard Error of the Mean]]
 
 
|}
 
|}
  
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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)]
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*[[ZINC12 Database]]
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*[[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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| [[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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== 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]]
 
 
|}
 
|}
 +
 +
== AutoDock4 ==
 +
{|
 +
*[[AutoDock4 Pose Reproduction Tutorial]]
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*[[AutoDock4 Crossdock]]
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*[[AutoDock4 Benchmark Results]]
 +
|}
 +
 +
== AutoDock Vina ==
 +
{|
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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 purchase compounds for Rizzo lab]]
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| [[CVS Commands]]
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* [[X-Win32]]  
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| [[Ethernet Cables]]
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* [[CVS Commands]]
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| [[Sequence alignment]]  
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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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| [[Making images for publication]]
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* [[Lab-designed code and programs]]
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| [[Lab-designed code and programs]]
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* [[Server Administration]]
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| [[Server Administration]]
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* [[Amber on Seawulf (compilation)]]
−
|-
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* [[Cluster compilations]]
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| [[Amber on Seawulf (compilation)]]
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* [[NAMD on Seawulf]]
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| [[Cluster compilations]]
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* [[Semester Checklist]]
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| [[NAMD on Seawulf]]
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* [[Wiki Editing]]
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| [[Dell 5110cn Printer]]
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*[[Other Meetings]]
−
|-
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*[[Seawulf Cluster Assessment]]
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| [[Semester Checklist]]
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*[[Formatting your Thesis]]
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| [[Wiki Editing]]
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*[[Setting up insurance through Research Foundation]]
−
|-
 
−
|[[Stony Brook Joint Group Meetings in Computational Structural Biology]]
 
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|[[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 09:56, 16 June 2021

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

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