MMTSB
Tool Set Documentation

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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 (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