|
|
Difference between revisions of "Main Page"
From MMTSB
| Line 10: | Line 10: | ||
|- | |- | ||
| <TT>[[mutateNA.pl]]</TT> || (nucleotide mutations) | | <TT>[[mutateNA.pl]]</TT> || (nucleotide mutations) | ||
| − | | | + | |} |
== Structure analysis == | == Structure analysis == | ||
| − | + | {| | |
|- | |- | ||
| <TT>[[centerOfMass.pl]]</TT> || (center of mass) | | <TT>[[centerOfMass.pl]]</TT> || (center of mass) | ||
| Line 41: | Line 41: | ||
== All-Atom Modeling == | == All-Atom Modeling == | ||
| − | + | {| | |
| − | + | |- | |
| − | + | | <TT>[[enerCHARMM.pl]]</TT> || (evaluate energy with CHARMM) | |
| − | + | |- | |
| − | + | | <TT>[[minCHARMM.pl]]</TT> || (minimize with CHARMM) | |
| − | + | |- | |
| − | + | | <TT>[[mdCHARMM.pl]]</TT> || (run molecular dynamics with CHARMM) | |
| − | + | |- | |
| − | + | | <TT>[[analyzeCHARMM.pl]]</TT> || (analyze molecular dynamics simulations with CHARMM) | |
| − | + | |- | |
| − | + | | <TT>[[nmaCHARMM.pl]]</TT> || (normal mode analysis with CHARMM) | |
| − | + | |- | |
| − | + | | <TT>[[pbCHARMM.pl]]</TT> || (Poisson-Boltzmann calculations with CHARMM) | |
| − | + | |- | |
| + | | <TT>[[equiCHARMM.pl]]</TT> || (explicit solvent simulations equilibration) | ||
| + | |- | ||
| + | | <TT>[[scalarCHARMM.pl]]</TT> || (obtain scalar variables from CHARMM) | ||
| + | |- | ||
| + | | <TT>[[genPSF.pl]]</TT> || (generate PSF file from PDB) | ||
| + | |- | ||
| + | | <TT>[[pdb2traj.pl]]</TT> || (generate DCD trajectory from list of PDBs) | ||
| + | |- | ||
| + | | <TT>[[processDCD.pl]]</TT> || (process DCD trajectory file) | ||
| + | |} | ||
| + | |||
| + | {| | ||
| + | |- | ||
| + | | <TT>[[enerAmber.pl]]</TT> || (evaluate energy with Amber) | ||
| + | |- | ||
| + | | <TT>[[minAmber.pl]]</TT> || (minimize with Amber) | ||
| + | |- | ||
| + | | <TT>[[mdAmber.pl]]</TT> || (run molecular dynamics simulation with Amber) | ||
| + | |} | ||
== SICHO Lattice Modeling == | == SICHO Lattice Modeling == | ||
Revision as of 21:21, 11 August 2006
Structure preparation
| convpdb.pl | (conversion/manipulation of PDB files) |
| complete.pl | (completion of missing atoms) |
| mutate.pl | (amino acid residue mutations) |
| mutateNA.pl | (nucleotide mutations) |
Structure analysis
| centerOfMass.pl | (center of mass) |
| rgyr.pl | (radius of gyration) |
| rms.pl | (root mean square displacement) |
| lsqfit.pl | (least-squares fit superposition) |
| contact.pl | (identification and comparison of native contacts) |
| countIntCont.pl | (contacts between different chains) |
| mindist.pl | (minimum distance between two residues) |
| qscore.pl | (Q-score calculation) |
| dihed.pl | (phi/psi/chi1 dihedral calculation) |
| vicinity.pl | (identification of residues within cutoff) |
| cluster.pl | (clustering based on mutual similarity) |
All-Atom Modeling
| enerCHARMM.pl | (evaluate energy with CHARMM) |
| minCHARMM.pl | (minimize with CHARMM) |
| mdCHARMM.pl | (run molecular dynamics with CHARMM) |
| analyzeCHARMM.pl | (analyze molecular dynamics simulations with CHARMM) |
| nmaCHARMM.pl | (normal mode analysis with CHARMM) |
| pbCHARMM.pl | (Poisson-Boltzmann calculations with CHARMM) |
| equiCHARMM.pl | (explicit solvent simulations equilibration) |
| scalarCHARMM.pl | (obtain scalar variables from CHARMM) |
| genPSF.pl | (generate PSF file from PDB) |
| pdb2traj.pl | (generate DCD trajectory from list of PDBs) |
| processDCD.pl | (process DCD trajectory file) |
| enerAmber.pl | (evaluate energy with Amber) |
| minAmber.pl | (minimize with Amber) |
| mdAmber.pl | (run molecular dynamics simulation with Amber) |
SICHO Lattice Modeling
genchain.pl geninput.pl checkchain.pl genrestr.pl genseq.pl hlamc.pl latticeener.pl latticesim.pl rebuild.pl xtracttra.pl
Replica Exchange Sampling
aarex.pl aarexAmaber.pl latrex.pl gorex.pl hlamcrex.pl readArchive.pl rexanalysis.pl rexinfo.pl rexserver.pl writeArchive.pl
Ensemble Computing
bestcluster.pl calcprop.pl checkin.pl enscluster.pl enscut.pl enseval.pl ensfiles.pl enslatsim.pl ensmin.pl ensrun.pl getprop.pl showcluster.pl jobserver.pl setprop.pl
Structure Prediction
buildModel.pl psiblast.pl psipred.pl