Difference between revisions of "Rizzo Lab Information and Tutorials"
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| + | == DOCK == | ||
| + | {| cellpadding=0 width=90% | ||
| + | *[http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm Online Users Manual] | ||
| + | *[[Tutorials]] | ||
| + | ** virtual screen, de novo design, genetic algorithm, covalent | ||
| + | *[[Benchmarking Protocols and Results]] | ||
| + | ** testset, pose reproduction, crossdocking, database enrichment SOP and other algorithm results | ||
| + | *[[Additional DOCK6 Information]] | ||
| + | ** miscellaneous information for DOCK scoring functions and experiments (some legacy) | ||
| + | |} | ||
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== Visualization Software == | == Visualization Software == | ||
*[[Chimera]] | *[[Chimera]] | ||
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== Basic Linux Tools== | == Basic Linux Tools== | ||
{| cellpadding=0 width=90% | {| cellpadding=0 width=90% | ||
| − | + | *[[Unix]] | |
| − | + | *[[vi ]] | |
| − | + | *[[sed - Stream Editor in Unix]] | |
| − | + | *[[Slick awk tricks]] | |
| − | + | *[[Ways to remove the first line]] | |
| − | + | *[[PBS Queue]] | |
| − | + | *[[Useful Slurm Commands]] | |
| − | + | *[[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]] | ||
|} | |} | ||
| − | == | + | == Molecular Dynamics == |
{| cellpadding=0 width=90% | {| cellpadding=0 width=90% | ||
| − | + | *[[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 == |
{| cellpadding=0 width=90% | {| cellpadding=0 width=90% | ||
| − | + | * [[Compiling GROMACS on Cluster]] | |
| − | + | * [[MD Simulation: Protein in Water]] | |
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|} | |} | ||
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== Monte Carlo == | == Monte Carlo == | ||
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== Analysis Tools == | == Analysis Tools == | ||
| + | * [[Analysis Tools Repository]] | ||
* [[MATLAB]] | * [[MATLAB]] | ||
* [[Octave]] | * [[Octave]] | ||
* [[R - Statistical Computing]] | * [[R - Statistical Computing]] | ||
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* [[gnuplot]] | * [[gnuplot]] | ||
* [[pylab]] | * [[pylab]] | ||
== Databases == | == Databases == | ||
| − | *[http:// | + | *[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)] | ||
| − | *[ | + | *[[ZINC12 Database]] |
| + | *[[ZINC15 Database]] | ||
*[[Families in the Protein Databank]] | *[[Families in the Protein Databank]] | ||
| + | *[[Automated Family generation from PDB]] | ||
*[[Drug-like organic molecules]] | *[[Drug-like organic molecules]] | ||
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== Conversion between file types == | == Conversion between file types == | ||
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* [[NAMD to mol2 ]] | * [[NAMD to mol2 ]] | ||
* [[pdb to mol2]] | * [[pdb to mol2]] | ||
| − | + | * [[SDF to mol2]] | |
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Latest revision as of 10:50, 25 March 2024
Contents
DOCK
Visualization Software
Basic Linux Tools
Molecular Dynamics
GROMACS
Monte Carlo
Analysis Tools
Databases
- PubChem (ligand database)
- NIST (small molecule database)
- ZINC12 Database
- ZINC15 Database
- Families in the Protein Databank
- Automated Family generation from PDB
- Drug-like organic molecules
