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Main Page
From MMTSB
Structure preparation
| convpdb.pl | conversion/manipulation of PDB files |
| complete.pl | completion of missing atoms |
| mutate.pl | amino acid residue mutations |
| mutateNA.pl | nucleotide base 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
| enerCHARMM.pl | evaluate energy with CHARMM |
| minCHARMM.pl | minimize with CHARMM |
| mdCHARMM.pl | run molecular dynamics with CHARMM |
| analyzeCHARMM.pl | analyze molecular dynamics simulations with CHARMM |
| nmaCHARMM.pl | normal mode analysis with CHARMM |
| pbCHARMM.pl | Poisson-Boltzmann calculations with CHARMM |
| equiCHARMM.pl | explicit solvent simulations equilibration |
| scalarCHARMM.pl | obtain scalar variables from CHARMM |
| genPSF.pl | generate PSF file from PDB |
| pdb2traj.pl | generate DCD trajectory from list of PDBs |
| processDCD.pl | process DCD trajectory file |
| enerAmber.pl | evaluate energy with Amber |
| minAmber.pl | minimize with Amber |
| mdAmber.pl | run molecular dynamics simulation with Amber |
SICHO Lattice Modeling
| latticesim.pl | SICHO lattice simulation with MONSSTER |
| latticeener.pl | SICHO energy from MONSSTER |
| genchain.pl | generate lattice chain from PDB |
| rebuild.pl | rebuild all-atom model from lattice chain |
| checkchain.pl | (check validity of lattice chain) |
| genseq.pl | (generate MONSSTER sequence file) |
| geninput.pl | (generate MONSSTER input file) |
| genrestr.pl | (generate MONSSTER restraint file) |
| xtracttra.pl | (extract lattice chain from MONSSTER trajectory) |
| hlamc.pl | (multi-scale lattice/all-atom sampling) |
Replica Exchange Sampling
| aarex.pl | (all-atom replica exchange simulation with CHARMM) |
| aarexAmber.pl | (all-atom replica exchange simulation with Amber) |
| latrex.pl | (lattice replica exchange simulation with MONSSTER) |
| gorex.pl | (GO model replica exchange simulation with CHARMM) |
| hlamcrex.pl | (multi-scale lattice/all-atom replica exchange simulation) |
| rexinfo.pl | (replica exchange control information) |
| rexanalysis.pl | (replica exchange analysis) |
| readArchive.pl | (read replica exchange trajectory archive file) |
| writeArchive.pl | (write replica exchange trajectory archive file) |
| rexserver.pl | (replica exchange server) |
Ensemble Computing
| checkin.pl | (generate ensemble from PDB files) |
| ensrun.pl | (run command across ensemble) |
| ensmin.pl | (minimize ensemble structures) |
| enseval.pl | (evaluate energy for members of ensemble) |
| enslatsim.pl | (generate ensemble from lattice simulations) |
| enscut.pl | (truncate residues of all members of ensemble) |
| ensfiles.pl | (obtain list of files for ensemble structures) |
| getprop.pl | (obtain data items for ensemble structures) |
| setprop.pl | (set data items for ensemble structures) |
| calcprop.pl | (calculate standard structural properties for ensemble) |
| enscluster.pl | (cluster ensemble structures) |
| bestcluster.pl | (rank clusters) |
| showcluster.pl | (display clusters) |
| jobserver.pl | (start job server for parallel runs) |
Structure Prediction
| buildModel.pl | (build template-based model with loops generated by MODELLER) |
| psipred.pl | (predict secondary structure with PSIPRED) |
| psiblast.pl | (obtain sequence alignment with PSI-BLAST) |