Difference between revisions of "Rizzo Lab Information and Tutorials"
From Rizzo_Lab
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|[[Protein-Ligand Complex MD]] | |[[Protein-Ligand Complex MD]] | ||
|[[Membrane Protein MD]] | |[[Membrane Protein MD]] | ||
Revision as of 17:26, 19 July 2011
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 | 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
| Compiling GROMACS on Cluster | ||
| MD of Protein in Water | Protein-Ligand Complex MD | Membrane Protein MD |
| TI: Mutating Ligand to Nothing | TI: Mutating Ligand to Ligand | Steered MD / Umbrella Sampling |
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 |
