A   Amber.pm Interface to Amber program   Analyze.pm Analyze protein structures   aarex.pl All-atom replica exchange simulations (MD)   aarexAmber.pl All-atom replica exchange simulations with Amber (MD) B   bestcluster.pl Best clusters C   CHARMM.pm Interface to CHARMM program   Client.pm Generic client for parallel job execution   Cluster.pm Cluster protein structures   calcprop.pl Calculate properties for ensemble   checkchain.pl Check validity of SICHO lattice chain for use with MONSSTER   checkin.pl Check lattice chains or PDB files into ensemble   cluster.pl Clustering of structures   complete.pl Add hydrogens and other missing atoms to protein structure   contact.pl Residue contact map   convpdb.pl Convert, renumber, and clean-up protein PDB files D   dihed.pl Phi/Psi/Chi1 dihedral distribution E   Ensemble.pm Manage simulation ensembles   enerAmber.pl Evaluate Amber energy   enerCHARMM.pl Evaluate CHARMM energy   enscluster.pl Clustering of ensemble structures   enscut.pl Cut out protein structures around fragments/loops   enseval.pl Ensemble energy evaluations   ensfiles.pl List of files from ensemble structures   enslatsim.pl Run ensemble lattice simulations   ensmin.pl Run ensemble minimizations   ensrun.pl Run user command for ensemble structures   evaluate.pl Evaluate a set of PDB files G   GenUtil.pm Various utilities for internal use   genchain.pl Generate SICHO lattice chain from PDB   geninput.pl Generate MONSSTER input file   genrestr.pl Generate MONSSTER restraint file   genseq.pl Generate MONSSTER sequence file   getprop.pl Retrieve properties for ensemble structures   gorex.pl Ca-atom (Go-model) replica exchange simulations (MD) H   hlamc.pl Single lattice/all-atom simulations   hlamcrex.pl Replica exchange lattice sampling on all-atom surface J   JobClient.pm Client for parallel ensemble jobs   JobServer.pm Server for parallel ensemble jobs   jclust Hierarchical clustering   jobserver.pl Job server for parallel ensemble runs K   kclust Optimizing fixed radius clustering L   LatEnsemble.pm Manage lattice simulation ensembles   LatSimReXServer.pm Replica exchange server for lattice simulations   latrex.pl Lattice replica exchange simulations (MC)   latticeener.pl Evaluates the SICHO energy for a lattice chain   latticesim.pl Run lattice simulations with MONSSTER   lsqfit.pl Align protein structures by least squares fit M   MONSSTER.pm Interface to MONSSTER program   Molecule.pm Manage all-atom molecules   mchain Generate SICHO lattice chains for MONSSTER   mdAmber.pl Run molecular dynamics with Amber   mdCHARMM.pl Run molecular dynamics with CHARMM   minAmber.pl Minimize all-atom model with Amber   minCHARMM.pl Minimize all-atom model with CHARMM   mindist.pl Minimum distance between two residues   mutate.pl Mutate residues in a given structure P   pbCHARMM.pl Evaluate Poisson-Boltzmann energies   predict.pl Structure refinement/prediction Q   qscore.pl Q score calculation R   ReXClient.pm Replica exchange client   ReXServer.pm Replica exchange server   readArchive.pl Extract data from archive file   rebuild Rebuild all-atom structures from lattice chains   rebuild.pl Rebuild all-atom model from SICHO lattice chain   rexinfo.pl Extract replica exchange data   rexserver.pl Server for replica exchange simulations   rgyr.pl Radius of gyration   rms.pl Calculate RMSD values between two protein structures S   SICHO.pm Manage SICHO models   Sequence.pm Manage protein sequences   Server.pm Generic server for parallel job execution   SimData.pm Manage simulation data for ensembles   setprop.pl Set properties for ensemble   showcluster.pl List clusters V   vicinity.pl Find residues in vicinity of fragment W   writeArchive.pl Add data to archive file X   xtracttra.pl Extract lattice chain from MONSSTER trajectory file