Difference between revisions of "Rizzo Lab Information and Tutorials"

From Rizzo_Lab
Jump to: navigation, search
(DOCKing)
 
(137 intermediate revisions by 12 users not shown)
Line 1: Line 1:
 +
== DOCK ==
 +
{| cellpadding=0 width=90%
 +
*[http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm Online Users Manual]
 +
*[[Tutorials]]
 +
*[[Benchmarking]]
 +
*[[Developer's Info]]
 +
*[[Testset Protocols]]
 +
*[[Parameter List/Explanations]]
 +
*[[Scoring Functions]]
 +
*[[Example Input Files]]
 +
*[[DOCK Abbreviations Guide]]
 +
*[[Advanced Dock Utilities/Information]]
 +
*[[DOCK6 POSE Reproduction]]
 +
*[[Virtual Screening SOP]]
 +
|}
 +
 
== Visualization Software ==
 
== Visualization Software ==
 
*[[Chimera]]
 
*[[Chimera]]
Line 6: Line 22:
 
== Basic Linux Tools==
 
== Basic Linux Tools==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
|[[Unix]]
+
*[[Unix]]
|[[vi ]]
+
*[[vi ]]
|[[sed - Stream Editor in Unix]]
+
*[[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]]
+
*[[gdb (GNU Debugger)]]
|-
+
*[[Common Errors - ctrl M]]
|[[gdb (GNU Debugger)]]
+
*[[C Shell Scripting]]
|[[Common Errors - ctrl M]]
+
*[[Unix find]]
|[[C Shell Scripting]]
+
*[[Which Unix Distribution?]]
|-
+
*[[rsync]]
|[[Unix find]]
+
*[[MPICH]]
|[[Which Unix Distribution?]]
+
*[[Secure Shell (ssh)]]
|[[rsync]]
+
*[[Archiving old data]]
|-
+
*[[valgrind]]
|[[MPICH]]
+
*[[Ghostscript]]
|[[Secure Shell (ssh)]]
 
|[[Archiving old data]]
 
|-
 
|[[valgrind]]
 
|[[Ghostscript]]
 
|}
 
 
 
== Virtual Screening Protocol on BlueGene ==
 
Yulin Huang
 
In this document, the current Rizzo group protocol will be described in detail. This protocol has be through successive iterations and has be used to select compounds for Flu and HIVgp41 (number of purchased compounds for HIV = 112).
 
{| cellpadding=0 width=90%
 
|[[DOCK Tutorials]]
 
|[[Testset Protocols]]
 
|[[Scoring Functions]]
 
|[[Sampling Methods]]
 
|-
 
|[[ZINC Database]]
 
|[[Installing DOCK]]
 
|[[Optimize Polar Hydrogens]]
 
|[[Virtual Screening Protocol]]
 
|-
 
|[[Sphere Generation]]
 
|[[DOCK Compilation]]
 
 
|}
 
|}
  
 
== Molecular Dynamics ==
 
== Molecular Dynamics ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
|[[AMBER Tutorials]]
+
*[[AMBER Tutorials]]
|[[AMBER TI Tutorials]]
+
*[[AMBER TI Tutorials]]
|[[AMBER tricks]]
+
*[[AMBER Lipid Tutorials]]
|-
+
*[[AMBER tricks]]
|[[NAMD tutorial]]
+
*[[NAMD tutorial]]
|[[NAMD Amber inputs]]
+
*[[NAMD Amber inputs]]
|-
+
*[[per-residue energy decompositions]]
|[[per-residue energy decompositions]]
+
*[[nonstandard residues prep]]
|[[nonstandard residues prep]]
+
*[[ptraj]]
|-
+
*[[Blocked Standard Error of the Mean]]
|[[ptraj]]
 
 
|}
 
|}
[http://www.ams.sunysb.edu/~tbalius/NamdandDockonNYBlue.pdf NAMD and DOCK on BlueGene ]
 
===error analysis===
 
[[Blocked Standard Error of the Mean]]
 
[[autocorrelation function]]
 
  
 
== GROMACS ==
 
== GROMACS ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
|[[Compiling GROMACS on Cluster]]
+
* [[Compiling GROMACS on Cluster]]
|-
+
* [[MD Simulation: Protein in Water]]
|[[MD Simulation: Protein in Water]]
+
|}
|[[MD Simulation: Protein-Ligand Complex]]
 
|[[Membrane Protein Systems]]
 
|-
 
|[[TI: Mutating Ligand to Nothing]]
 
|[[TI: Mutating Ligand to Ligand]]
 
|[[Steered MD / Umbrella Sampling]]
 
|-
 
|}
 
  
 
== Monte Carlo ==
 
== Monte Carlo ==
Line 85: Line 65:
  
 
== Analysis Tools ==
 
== Analysis Tools ==
 +
* [[Analysis Tools Repository]]
 
* [[MATLAB]]
 
* [[MATLAB]]
 
* [[Octave]]
 
* [[Octave]]
 
* [[R - Statistical Computing]]
 
* [[R - Statistical Computing]]
* [[Xmgrace]]
 
 
* [[gnuplot]]
 
* [[gnuplot]]
 
* [[pylab]]
 
* [[pylab]]
  
 
== Databases ==
 
== Databases ==
*[http://129.43.27.140/ncidb2/ NCI (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 ==
Line 124: Line 90:
 
== 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]]
+
 
 +
== AutoDock4 ==
 +
{|
 +
*[[AutoDock4 Pose Reproduction Tutorial]]
 +
*[[AutoDock4 Crossdock]]
 +
*[[AutoDock4 Benchmark Results]]
 
|}
 
|}
 +
 +
== AutoDock Vina ==
 +
{|
 +
*[[AutoDock Vina Pose Reproduction Tutorial]]
 +
*[[AutoDock Vina Benchmark Results]]
 +
|}
  
 
== Miscellaneous ==
 
== Miscellaneous ==
 
{| cellpadding=0 width=90%
 
{| cellpadding=0 width=90%
| [[X-Win32]]  
+
* [[How to purchase compounds for Rizzo lab]]
| [[CVS Commands]]
+
* [[X-Win32]]  
| [[Ethernet Cables]]
+
* [[CVS Commands]]
| [[Sequence alignment]]  
+
* [[Ethernet Cables]]
|-
+
* [[Sequence alignment]]  
| [[Visiting BNL]]
+
* [[Making images for publication]]
| [[Making images for publication]]
+
* [[Lab-designed code and programs]]
| [[Lab-designed code and programs]]
+
* [[Server Administration]]
| [[Server Administration]]
+
* [[Amber on Seawulf (compilation)]]
|-
+
* [[Cluster compilations]]
| [[Amber on Seawulf (compilation)]]
+
* [[NAMD on Seawulf]]
| [[Cluster compilations]]
+
* [[Semester Checklist]]
| [[NAMD on Seawulf]]
+
* [[Wiki Editing]]
| [[Dell 5110cn Printer]]
+
*[[Other Meetings]]
|-
+
*[[Seawulf Cluster Assessment]]
| [[Journal Articles from UCSF]]
+
*[[Formatting your Thesis]]
| [[Semester Checklist]]
+
*[[Setting up insurance through Research Foundation]]
 
|}
 
|}
  
== Insurance ==
+
==Archive==
[[Research Foundation]]
+
*[[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