Difference between revisions of "Rizzo Lab Information and Tutorials"
From Rizzo_Lab
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| − | == | + | == Virtual Screening Protocol on BlueGene == |
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| + | 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). | ||
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|[[DOCK Tutorials]] | |[[DOCK Tutorials]] | ||
Revision as of 17:31, 20 July 2012
Contents
Visualization Software
Basic Linux Tools
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).
| DOCK Tutorials | Testset Protocols | Scoring Functions | Sampling Methods |
| ZINC Database | Installing DOCK | Optimize Polar Hydrogens | Virtual Screening Protocol |
| Sphere Generation | DOCK Compilation |
Molecular Dynamics
| AMBER Tutorials | AMBER TI Tutorials | AMBER tricks |
| NAMD tutorial | NAMD Amber inputs | |
| per-residue energy decompositions | nonstandard residues prep | |
| ptraj |
error analysis
Blocked Standard Error of the Mean autocorrelation function
GROMACS
Monte Carlo
Analysis Tools
Databases
- NCI (ligand database)
- NIST (small molecule database)
- ZINC (ligand database)
- Families in the Protein Databank
- Automated Families generation from the Protein Databank
- Drug-like organic molecules
BlueGene
Conversion between file types
Setting up accounts
| Getting a BNL Account | Activating your Seawulf Account | Rotation students Wiki | Setting up RSA SecureID token |
