Difference between revisions of "Rizzo Lab Information and Tutorials"
From Rizzo_Lab
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| + | == DOCK == | ||
| + | {| cellpadding=0 width=90% | ||
| + | *[http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm Online Users Manual] | ||
| + | *[[Tutorials]] | ||
| + | *[[Benchmarking]] | ||
| + | *[[Testset Protocols]] | ||
| + | *[[Scoring Functions]] | ||
| + | *[[Sampling Methods]] | ||
| + | *[[Analog Library - Pubchem & Zinc]] | ||
| + | *[[ZINC12 Database]] | ||
| + | *[[ZINC15 Database]] | ||
| + | *[[DOCK Installation]] | ||
| + | *[[Optimize Polar Hydrogens]] | ||
| + | *[[Virtual Screening Protocol]] | ||
| + | *[[Footprint Plot Visualization]] | ||
| + | *[[Sphere Generation]] | ||
| + | *[[Release]] | ||
| + | |} | ||
| + | |||
== Visualization Software == | == Visualization Software == | ||
*[[Chimera]] | *[[Chimera]] | ||
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*[[valgrind]] | *[[valgrind]] | ||
*[[Ghostscript]] | *[[Ghostscript]] | ||
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Revision as of 11:21, 5 February 2019
Contents
[hide]DOCK
- Online Users Manual
- Tutorials
- Benchmarking
- Testset Protocols
- Scoring Functions
- Sampling Methods
- Analog Library - Pubchem & Zinc
- ZINC12 Database
- ZINC15 Database
- DOCK Installation
- Optimize Polar Hydrogens
- Virtual Screening Protocol
- Footprint Plot Visualization
- Sphere Generation
- Release
Visualization Software
Basic Linux Tools
- Unix
- vi
- sed - Stream Editor in Unix
- Slick awk tricks
- Ways to remove the first line
- PBS Queue
- gdb (GNU Debugger)
- Common Errors - ctrl M
- C Shell Scripting
- Unix find
- Which Unix Distribution?
- rsync
- MPICH
- Secure Shell (ssh)
- Archiving old data
- valgrind
- Ghostscript
De novo Design using DOCK
Molecular Dynamics
- AMBER Tutorials
- AMBER TI Tutorials
- AMBER Lipid Tutorials
- AMBER tricks
- NAMD tutorial
- NAMD Amber inputs
- per-residue energy decompositions
- nonstandard residues prep
- ptraj
- Blocked Standard Error of the Mean
GROMACS
Monte Carlo
Analysis Tools
Databases
- PubChem (ligand database)
- NIST (small molecule database)
- ZINC (ligand database)
- Families in the Protein Databank
- Automated Family generation from PDB
- Drug-like organic molecules
Conversion between file types
Setting up accounts
- Getting a BNL Account
- Activating your Seawulf Account
- Rotation students Wiki
- Setting up RSA SecureID token
Miscellaneous
- X-Win32
- CVS Commands
- Ethernet Cables
- Sequence alignment
- Making images for publication
- Lab-designed code and programs
- Server Administration
- Amber on Seawulf (compilation)
- Cluster compilations
- NAMD on Seawulf
- Semester Checklist
- Wiki Editing
- Other Meetings
- Seawulf Cluster Assessment
- Formatting your Thesis
- Setting up insurance through Research Foundation
