MMTSB
Tool Set Documentation

Difference between revisions of "Main Page"

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{|
 
{|
 
|-
 
|-
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|width=200pt| <TT>[[convpdb.pl]]</TT>  || (conversion/manipulation of PDB files)
+
|width=200pt| <TT>[[convpdb.pl]]</TT>  || conversion/manipulation of PDB files
 
|-
 
|-
−
| <TT>[[complete.pl]]</TT> || (completion of missing atoms)
+
| <TT>[[complete.pl]]</TT> || completion of missing atoms
 
|-
 
|-
−
| <TT>[[mutate.pl]]</TT>  || (amino acid residue mutations)
+
| <TT>[[mutate.pl]]</TT>  || amino acid residue mutations
 
|-
 
|-
−
| <TT>[[mutateNA.pl]]</TT> || (nucleotide mutations)
+
| <TT>[[mutateNA.pl]]</TT> || nucleotide base mutations
 
|}
 
|}
  
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{|
 
{|
 
|-
 
|-
−
| <TT>[[centerOfMass.pl]]</TT> || (center of mass)
+
|width=200pt| <TT>[[centerOfMass.pl]]</TT> || center of mass
 
|-
 
|-
−
| <TT>[[rgyr.pl]]</TT> || (radius of gyration)
+
| <TT>[[rgyr.pl]]</TT> || radius of gyration
 
|-
 
|-
−
| <TT>[[rms.pl]]</TT>  || (root mean square displacement)
+
| <TT>[[rms.pl]]</TT>  || root mean square displacement
 
|-
 
|-
−
| <TT>[[lsqfit.pl]]</TT> || (least-squares fit superposition)
+
| <TT>[[lsqfit.pl]]</TT> || least-squares fit superposition
 
|-
 
|-
−
| <TT>[[contact.pl]]</TT> || (identification and comparison of native contacts)
+
| <TT>[[contact.pl]]</TT> || identification and comparison of native contacts
 
|-
 
|-
−
| <TT>[[countIntCont.pl]]</TT> || (contacts between different chains)
+
| <TT>[[countIntCont.pl]]</TT> || contacts between different chains
 
|-
 
|-
−
| <TT>[[mindist.pl]]</TT> || (minimum distance between two residues)
+
| <TT>[[mindist.pl]]</TT> || minimum distance between two residues
 
|-
 
|-
−
| <TT>[[qscore.pl]]</TT> || (Q-score calculation)
+
| <TT>[[qscore.pl]]</TT> || Q-score calculation
 
|-
 
|-
−
| <TT>[[dihed.pl]]</TT> || (phi/psi/chi1 dihedral calculation)
+
| <TT>[[dihed.pl]]</TT> || phi/psi/chi1 dihedral calculation
 
|-
 
|-
−
| <TT>[[vicinity.pl]]</TT> || (identification of residues within cutoff)
+
| <TT>[[vicinity.pl]]</TT> || identification of residues within cutoff
 
|-  
 
|-  
−
| <TT>[[cluster.pl]]</TT> || (clustering based on mutual similarity)
+
| <TT>[[cluster.pl]]</TT> || clustering based on mutual similarity
 
|}
 
|}
  
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{|
 
{|
 
|-
 
|-
−
| <TT>[[enerCHARMM.pl]]</TT> || (evaluate energy with CHARMM)
+
|width=200pt| <TT>[[enerCHARMM.pl]]</TT> || evaluate energy with CHARMM
 
|-
 
|-
−
| <TT>[[minCHARMM.pl]]</TT> || (minimize with CHARMM)
+
| <TT>[[minCHARMM.pl]]</TT> || minimize with CHARMM
 
|-
 
|-
−
| <TT>[[mdCHARMM.pl]]</TT>  || (run molecular dynamics with CHARMM)
+
| <TT>[[mdCHARMM.pl]]</TT>  || run molecular dynamics with CHARMM
 
|-
 
|-
−
| <TT>[[analyzeCHARMM.pl]]</TT> || (analyze molecular dynamics simulations with CHARMM)
+
| <TT>[[analyzeCHARMM.pl]]</TT> || analyze molecular dynamics simulations with CHARMM
 
|-
 
|-
−
| <TT>[[nmaCHARMM.pl]]</TT> || (normal mode analysis with CHARMM)
+
| <TT>[[nmaCHARMM.pl]]</TT> || normal mode analysis with CHARMM
 
|-
 
|-
−
| <TT>[[pbCHARMM.pl]]</TT> || (Poisson-Boltzmann calculations with CHARMM)
+
| <TT>[[pbCHARMM.pl]]</TT> || Poisson-Boltzmann calculations with CHARMM
 
|-
 
|-
−
| <TT>[[equiCHARMM.pl]]</TT> || (explicit solvent simulations equilibration)
+
| <TT>[[equiCHARMM.pl]]</TT> || explicit solvent simulations equilibration
 
|-
 
|-
−
| <TT>[[scalarCHARMM.pl]]</TT> || (obtain scalar variables from CHARMM)
+
| <TT>[[scalarCHARMM.pl]]</TT> || obtain scalar variables from CHARMM
 
|-
 
|-
−
| <TT>[[genPSF.pl]]</TT> || (generate PSF file from PDB)
+
| <TT>[[genPSF.pl]]</TT> || generate PSF file from PDB
 
|-
 
|-
−
| <TT>[[pdb2traj.pl]]</TT> || (generate DCD trajectory from list of PDBs)
+
| <TT>[[pdb2traj.pl]]</TT> || generate DCD trajectory from list of PDBs
 
|-  
 
|-  
−
| <TT>[[processDCD.pl]]</TT> || (process DCD trajectory file)
+
| <TT>[[processDCD.pl]]</TT> || process DCD trajectory file
 
|-
 
|-
−
| <TT>[[enerAmber.pl]]</TT>  || (evaluate energy with Amber)
+
| <TT>[[enerAmber.pl]]</TT>  || evaluate energy with Amber
 
|-
 
|-
−
| <TT>[[minAmber.pl]]</TT> || (minimize with Amber)
+
| <TT>[[minAmber.pl]]</TT> || minimize with Amber
 
|-
 
|-
−
| <TT>[[mdAmber.pl]]</TT>  || (run molecular dynamics simulation with Amber)
+
| <TT>[[mdAmber.pl]]</TT>  || run molecular dynamics simulation with Amber
 
|}
 
|}
  
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{|
 
{|
 
|-
 
|-
−
| <TT>[[latticesim.pl]]</TT> || (SICHO lattice simulation with MONSSTER)
+
|width=200pt| <TT>[[latticesim.pl]]</TT> || SICHO lattice simulation with MONSSTER
 
|-
 
|-
−
| <TT>[[latticeener.pl]]</TT> || (SICHO energy from MONSSTER)
+
| <TT>[[latticeener.pl]]</TT> || SICHO energy from MONSSTER
 
|-
 
|-
−
| <TT>[[genchain.pl]]</TT>  || (generate lattice chain from PDB)
+
| <TT>[[genchain.pl]]</TT>  || generate lattice chain from PDB
 
|-
 
|-
−
| <TT>[[rebuild.pl]]</TT> || (rebuild all-atom model from lattice chain)
+
| <TT>[[rebuild.pl]]</TT> || rebuild all-atom model from lattice chain
 
|-
 
|-
 
| <TT>[[checkchain.pl]]</TT> || (check validity of lattice chain)
 
| <TT>[[checkchain.pl]]</TT> || (check validity of lattice chain)

Revision as of 13:20, 12 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 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)
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