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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*[[Example Input Files]]
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*[[Advanced Dock Utilities/Information]]
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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]]
 
 
*[[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]]
 
 
*[[Activating your Seawulf Account]]
 
*[[Activating your Seawulf Account]]
 
*[[Rotation students Wiki]]
 
*[[Rotation students Wiki]]
*[[Setting up RSA SecureID token]]
 
 
|}
 
|}
  
 
== Miscellaneous ==
 
== Miscellaneous ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
*[[X-Win32]]  
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* [[How to write Makefiles]]
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* [[X-Win32]]  
 
* [[CVS Commands]]
 
* [[CVS Commands]]
 
* [[Ethernet Cables]]
 
* [[Ethernet Cables]]
 
* [[Sequence alignment]]  
 
* [[Sequence alignment]]  
* [[Visiting BNL]]
 
 
* [[Making images for publication]]
 
* [[Making images for publication]]
 
* [[Lab-designed code and programs]]
 
* [[Lab-designed code and programs]]
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* [[Cluster compilations]]
 
* [[Cluster compilations]]
 
* [[NAMD on Seawulf]]
 
* [[NAMD on Seawulf]]
*[[Dell 5110cn Printer]]
 
 
* [[Semester Checklist]]
 
* [[Semester Checklist]]
 
* [[Wiki Editing]]
 
* [[Wiki Editing]]
*[[Stony Brook Joint Group Meetings in Computational Structural Biology]]
 
 
*[[Other Meetings]]
 
*[[Other Meetings]]
 
*[[Seawulf Cluster Assessment]]
 
*[[Seawulf Cluster Assessment]]

Latest revision as of 16:46, 23 January 2020

DOCK

Visualization Software

Basic Linux Tools

Molecular Dynamics

GROMACS

Monte Carlo

Analysis Tools

Databases

Conversion between file types

Setting up accounts

Miscellaneous

Archive