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NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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Unread 06-12-2005, 03:21 AM
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The following Perl scripts for Amber-driven NMR structure determination are available from the website of Dr. Gorenstein:
  • carnal.aveminclusters.in Calculates the average structure from sander restrt files and
    calculates the RMSD for each vs. the average structure.
  • addcio.pl Add Na+ counterions to DNA
  • amber_2_charm.pl
  • amber_dna_pdb_to_star.pl
  • amber_pdb_to_star.pl
  • amber_protein_pdb_to_star.pl
  • average_starpdb.pl Calculates an average PDB from an RCSB ensemble.
  • talos_to_amber_restr.pl Creates AMBER dihedral restraints from a TALOS program prediction table. Only the restraints designated as "Good" are converted.
  • distance_matrix.pl Create a text file showing all proton-proton distances less than 5 Angstroms from a model PDB structure.
  • HA_HA_distance.pl Finds all HA-HA distances less than 3.5 Angstrom (cutoff can be changed).
  • comp_listout.pl Compare Sander listout files for recurring bad noes.
  • g98allpdbs.pl Converts a Gaussian98.out file (with XYZ coord) into multiple PDB files.
    This is usefule for making a movie of a calculation.
  • g98xyztoPDB.pl Creates a PDB file from the LAST coordinates of a Gaussian 98 output file.
  • gvxyzcom_2_pdb.pl Converts a GaussView.com file (with XYZ coords) to a PDB file.
  • listout_noesy_sorter.pl Counts and sorts sander listout file into intra, seq., medium and long range NOES.
  • make_protein_dihedrals.pl Makes AMBER format angle restraints for Helices and Beta Sheets.
  • make_ribose_dihedrals.pl Makes B-DNA AMBER dihedral restraints.
  • vnmr2morassfinal.pl Convert assigned VNMR 2D peak file into a MORASS program input file.
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