|
|
Difference between revisions of "Main Page"
From MMTSB
| Line 14: | Line 14: | ||
== Structure analysis == | == Structure analysis == | ||
| − | centerOfMass.pl | + | {| |
| − | + | |- | |
| − | + | | <TT>[[centerOfMass.pl]]</TT> || (center of mass) | |
| − | + | |- | |
| − | + | | <TT>[[rgyr.pl]]</TT> || (radius of gyration) | |
| − | + | |- | |
| − | mindist.pl | + | | <TT>[[rms.pl]]</TT> || (root mean square displacement) |
| − | qscore.pl | + | |- |
| − | + | | <TT>[[lsqfit.pl]]</TT> || (least-squares fit superposition) | |
| − | + | |- | |
| − | + | | <TT>[[contact.pl]]</TT> || (identification and comparison of native contacts) | |
| + | |- | ||
| + | | <TT>[[countIntCont.pl]]</TT> || (contacts between different chains) | ||
| + | |- | ||
| + | | <TT>[[mindist.pl]]</TT> || (minimum distance between two residues) | ||
| + | |- | ||
| + | | <TT>[[qscore.pl]]</TT> || (Q-score calculation) | ||
| + | |- | ||
| + | | <TT>[[dihed.pl]]</TT> || (phi/psi/chi1 dihedral calculation) | ||
| + | |- | ||
| + | | <TT>[[vicinity.pl]]</TT> || (identification of residues within cutoff) | ||
| + | |- | ||
| + | | <TT>[[cluster.pl]]</TT> || (clustering based on mutual similarity) | ||
| + | |} | ||
== All-Atom Modeling == | == All-Atom Modeling == | ||
Revision as of 21:10, 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
enerAmber.pl enerCHARMM.pl analyzeCHARMM.pl equiCHARMM.pl genPSF.pl mdAmber.pl mdCHARMM.pl minAmber.pl minCHARMM.pl nmaCHARMM.pl pbCHARMM.pl pdb2traj.pl processDCD.pl scalarCHARMM.pl
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