|
|
Difference between revisions of "Main Page"
From MMTSB
| Line 74: | Line 74: | ||
== SICHO Lattice Modeling == | == SICHO Lattice Modeling == | ||
| − | + | {| | |
| − | + | |- | |
| − | + | | <TT>[[latticesim.pl]]</TT> || (SICHO lattice simulation with MONSSTER) | |
| − | + | |- | |
| − | + | | <TT>[[latticeener.pl]]</TT> || (SICHO energy from MONSSTER) | |
| − | + | |- | |
| − | + | | <TT>[[genchain.pl]]</TT> || (generate lattice chain from PDB) | |
| − | + | |- | |
| − | + | | <TT>[[rebuild.pl]]</TT> || (rebuild all-atom model from lattice chain) | |
| − | + | |- | |
| + | | <TT>[[checkchain.pl]]</TT> || (check validity of lattice chain) | ||
| + | |- | ||
| + | | <TT>[[genseq.pl]]</TT> || (generate MONSSTER sequence file) | ||
| + | |- | ||
| + | | <TT>[[geninput.pl]]</TT> || (generate MONSSTER input file) | ||
| + | |- | ||
| + | | <TT>[[genrestr.pl]]</TT> || (generate MONSSTER restraint file) | ||
| + | |- | ||
| + | | <TT>[[xtracttra.pl]]</TT> || (extract lattice chain from MONSSTER trajectory) | ||
| + | |- | ||
| + | | <TT>[[hlamc.pl]]</TT> || (multi-scale lattice/all-atom sampling) | ||
| + | |} | ||
== Replica Exchange Sampling == | == Replica Exchange Sampling == | ||
| − | aarex.pl | + | {| |
| − | + | |- | |
| − | latrex.pl | + | | <TT>[[aarex.pl]]</TT> || (all-atom replica exchange simulation with CHARMM) |
| − | gorex.pl | + | |- |
| − | hlamcrex.pl | + | | <TT>[[aarexAmber.pl]]</TT> || (all-atom replica exchange simulation with Amber) |
| − | + | |- | |
| − | rexanalysis.pl | + | | <TT>[[latrex.pl]]</TT> || (lattice replica exchange simulation with MONSSTER) |
| − | + | |- | |
| − | + | | <TT>[[gorex.pl]]</TT> || (GO model replica exchange simulation with CHARMM) | |
| − | writeArchive.pl | + | |- |
| − | + | | <TT>[[hlamcrex.pl]]</TT> || (multi-scale lattice/all-atom replica exchange simulation) | |
| − | + | |- | |
| − | + | | <TT>[[rexinfo.pl]]</TT> || (replica exchange control information) | |
| + | |- | ||
| + | | <TT>[[rexanalysis.pl]]</TT> || (replica exchange analysis) | ||
| + | |- | ||
| + | | <TT>[[readArchive.pl]]</TT> || (read replica exchange trajectory archive file) | ||
| + | |- | ||
| + | | <TT>[[writeArchive.pl]]</TT> || (write replica exchange trajectory archive file) | ||
| + | |- | ||
| + | | <TT>[[rexserver.pl]]</TT> || (replica exchange server) | ||
| + | |} | ||
== Ensemble Computing == | == Ensemble Computing == | ||
| − | + | {| | |
| − | + | |- | |
| − | + | | <TT>[[checkin.pl]]</TT> || (generate ensemble from PDB files) | |
| − | + | |- | |
| − | + | | <TT>[[ensrun.pl]]</TT> || (run command across ensemble) | |
| − | + | |- | |
| − | ensfiles.pl | + | | <TT>[[ensmin.pl]]</TT> || (minimize ensemble structures) |
| − | + | |- | |
| − | + | | <TT>[[enseval.pl]]</TT> || (evaluate energy for members of ensemble) | |
| − | + | |- | |
| − | + | | <TT>[[enslatsim.pl]]</TT> || (generate ensemble from lattice simulations) | |
| − | + | |- | |
| − | + | | <TT>[[enscut.pl]]</TT> || (truncate residues of all members of ensemble) | |
| − | + | |- | |
| − | + | | <TT>[[ensfiles.pl]]</TT> || (obtain list of files for ensemble structures) | |
| + | |- | ||
| + | | <TT>[[getprop.pl]]</TT> || (obtain data items for ensemble structures) | ||
| + | |- | ||
| + | | <TT>[[setprop.pl]]</TT> || (set data items for ensemble structures) | ||
| + | |- | ||
| + | | <TT>[[calcprop.pl]]</TT> || (calculate standard structural properties for ensemble) | ||
| + | |- | ||
| + | | <TT>[[enscluster.pl]]</TT> || (cluster ensemble structures) | ||
| + | |- | ||
| + | | <TT>[[bestcluster.pl]]</TT> || (rank clusters) | ||
| + | |- | ||
| + | | <TT>[[showcluster.pl]]</TT> || (display clusters) | ||
| + | |- | ||
| + | | <TT>[[jobserver.pl]]</TT> || (start job server for parallel runs) | ||
| + | |} | ||
== Structure Prediction == | == Structure Prediction == | ||
| − | + | {| | |
| − | buildModel.pl | + | |- |
| − | + | | <TT>[[buildModel.pl]]</TT> || (build template-based model with loops generated by MODELLER) | |
| − | + | |- | |
| + | | <TT>[[psipred.pl]]</TT> || (predict secondary structure with PSIPRED) | ||
| + | |- | ||
| + | | <TT>[[psiblast.pl]]</TT> || (obtain sequence alignment with PSI-BLAST) | ||
| + | |} | ||
Revision as of 21:44, 11 August 2006
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
| 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) |