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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 cluster.pl contact.pl countIntCont.pl dihed.pl lsqfit.pl mindist.pl qscore.pl rgyr.pl rms.pl vicinity.pl

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