Difference between revisions of "Rizzo Lab Information and Tutorials"
From Rizzo_Lab
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[http://www.ams.sunysb.edu/~tbalius/NamdandDockonNYBlue.pdf NAMD and DOCK on BlueGene ] | [http://www.ams.sunysb.edu/~tbalius/NamdandDockonNYBlue.pdf NAMD and DOCK on BlueGene ] | ||
| + | ===error analysis=== | ||
| + | Blocked Standard error of the Mean | ||
== Monte Carlo == | == Monte Carlo == | ||
Revision as of 13:05, 19 October 2010
Contents
Visualization Software
Basic Linux Tools
DOCKing
| DOCK Tutorials | Testset Protocols | Scoring Functions | Sampling Methods |
| ZINC Database | Installing DOCK | Optimize Polar Hydrogens | Virtual Screening Protocol |
| Sphere Generation |
Molecular Dynamics
| AMBER Tutorials | AMBER TI Tutorials | AMBER tricks |
| NAMD tutorial | NAMD Amber inputs | |
| ptraj |
error analysis
Blocked Standard error of the Mean
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 |
