Modeling Applications evaluate.pl Evaluate a set of PDB files predict.pl Structure refinement/prediction Lattice Modeling latticesim.pl Run lattice simulations with MONSSTER latticeener.pl Evaluates the SICHO energy for a lattice chain genchain.pl Generate SICHO lattice chain from PDB genseq.pl Generate MONSSTER sequence file geninput.pl Generate MONSSTER input file genrestr.pl Generate MONSSTER restraint file checkchain.pl Check validity of SICHO lattice chain for use with MONSSTER xtracttra.pl Extract lattice chain from MONSSTER trajectory file enslatsim.pl Run ensemble lattice simulations latrex.pl Lattice replica exchange simulations (MC) All-Atom Modeling rebuild.pl Rebuild all-atom model from SICHO lattice chain complete.pl Add hydrogens and other missing atoms to protein structure mutate.pl Mutate residues in a given structure minCHARMM.pl Minimize all-atom model with CHARMM enerCHARMM.pl Evaluate CHARMM energy pbCHARMM.pl Evaluate Poisson-Boltzmann energies mdCHARMM.pl Run molecular dynamics with CHARMM enerAmber.pl Evaluate Amber energy minAmber.pl Minimize all-atom model with Amber mdAmber.pl Run molecular dynamics with Amber convpdb.pl Convert, renumber, and clean-up protein PDB files vicinity.pl Find residues in vicinity of fragment ensmin.pl Run ensemble minimizations enseval.pl Ensemble energy evaluations enscut.pl Cut out protein structures around fragments/loops aarex.pl All-atom replica exchange simulations (MD) gorex.pl Ca-atom (Go-model) replica exchange simulations (MD) aarexAmber.pl All-atom replica exchange simulations with Amber (MD) Lattice/All-Atom Hybrid hlamc.pl Single lattice/all-atom simulations hlamcrex.pl Replica exchange lattice sampling on all-atom surface Protein Structure Analysis lsqfit.pl Align protein structures by least squares fit rms.pl Calculate RMSD values between two protein structures contact.pl Residue contact map mindist.pl Minimum distance between two residues rgyr.pl Radius of gyration dihed.pl Phi/Psi/Chi1 dihedral distribution qscore.pl Q score calculation calcprop.pl Calculate properties for ensemble cluster.pl Clustering of structures enscluster.pl Clustering of ensemble structures showcluster.pl List clusters bestcluster.pl Best clusters Structure Ensembles checkin.pl Check lattice chains or PDB files into ensemble calcprop.pl Calculate properties for ensemble setprop.pl Set properties for ensemble getprop.pl Retrieve properties for ensemble structures ensfiles.pl List of files from ensemble structures jobserver.pl Job server for parallel ensemble runs enslatsim.pl Run ensemble lattice simulations ensmin.pl Run ensemble minimizations enseval.pl Ensemble energy evaluations enscut.pl Cut out protein structures around fragments/loops ensrun.pl Run user command for ensemble structures cluster.pl Clustering of structures enscluster.pl Clustering of ensemble structures showcluster.pl List clusters bestcluster.pl Best clusters Replica Exchange Simulations rexserver.pl Server for replica exchange simulations aarex.pl All-atom replica exchange simulations (MD) aarexAmber.pl All-atom replica exchange simulations with Amber (MD) latrex.pl Lattice replica exchange simulations (MC) hlamcrex.pl Replica exchange lattice sampling on all-atom surface rexinfo.pl Extract replica exchange data readArchive.pl Extract data from archive file writeArchive.pl Add data to archive file