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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 03-26-2005, 06:18 AM
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The following Bruker pulse sequences can be found on BMRB website.

Shift correlation:

Homonuclear

Three-dimensional
  • TOCSY-HSQC 3D experiment
  • NOESY-HSQC 3D experiment
Heteronuclear

Two-dimensional
  • Bruker DMX 15N-1H 2D HSQC with Sensitivity-enhanced
  • Bruker AMX 15N-1H 2D HSQC with Sensitivity-enhanced
  • HMBC with gradient selection of echo and antiecho in t1 for suppression of t1-noise.
  • hsqc employing gradients for coherence selection. Phase sensitive by sampling +/- coherence in alternate scans.
  • selective hmbc with gradients; used when the selective 180 is greater than approx 1.5 ms
  • selective hmbc with gradients; used when the selective 180 is less than approx 1.5 ms
  • hsqc with selective 180(1H) pulses for high S/N
Three-dimensional
  • 3D HNCaCb - Gradient enhanced
  • 3D HNCaCb - Gradient enhanced with minimal H2O saturation
  • 3D HNCA with Gradient sensitivity enhancement with minimal H2O saturation
  • 3D HNCO with Gradient sensitivity enhancement with minimal H2O saturation
  • 3D HN(CO)CA with gradient sensitivity enhancement and minimal H2O saturation
  • 3D HCAN, gradient enhanced, deuterium decoupled
    - gradient program for previous pulse sequence
    - include file for previous pulse sequence
  • 3D HCA(CO)N, gradient enhanced, deuterium decoupled
    - gradient program for previous pulse sequence
    - include file for previous pulse sequence
Exchange spectroscopy (cross-relaxation and chemical exchange):

Homonuclear

One-dimensional
  • 13C edited (HMQC) 1D NOE difference JR for water suppression (9/27/95)
Two-dimensional
  • symmetrized CW-ROESY, program for DMX hardware, tested on DMX 500i and DMX750
Three-dimensional
  • Block-decoupled diagonal elements with spin diffusion eliminated 3D NOESY
  • Block-decoupled off-diagonal elements with spin diffusion eliminated 3D NOESY
Four-dimensional
  • 4D (13C,13C)-HMQC-NOESY-HSQC
Heteronuclear

Two-dimensional
  • 2D 1H/15N heteronuclear NOE with water along +Z
Three-dimensional
  • Bruker AMX 15N-1H 3D NOESY-HSQC with Sensitivity-enhanced
Relaxation

T1 Relaxation
  • DMX using States-TPPI
T1rho Relaxation
  • Off-resonance T1rho experiment
  • DMX using States-TPPI
J-coupling

Homonuclear

Two-dimensional
  • 2D difference 13C CT-HSQC for determination of J3(C'Cb) in Val, Ile, and Thr residues for the determination of X1 angle
Heteronuclear

Two-dimensional
  • Bruker DMX non-gradient 2D CT-HSQC; reference for 3D HNHB
  • Bruker DMX gradient 2D CT-HSQC; reference for 3D gradient HNHB
  • Auxiliary program needed by gradient 2D CT-HSQC
  • Measurement of 3J(HnHa) from a set of 2D J-modulated HMQC spectra.
  • 2D difference 13C CT-HSQC for determination of J3(NC) in Val, Ile, and Thr residues for the determination of X1 angle
Three-dimensional
  • Bruker DMX non-gradient 3D HNHB
  • Bruker DMX gradient 3D HNHB
  • Auxiliary program needed by gradient 3D HNHB
  • Measurement of 3J(HaC') from E.COSY splitting.
  • Measurement of 3J(HnCb) from E.COSY splitting.
  • Measurement of 3J(HnHa) from E.COSY splitting.
  • Measurement of C' to H J couplings from quantitative-type measurement.
Dipolar coupling

Heteronuclear

Two-dimensional
  • 2D IPAP [15N, 1H] HSQC
  • 2D IPAP HNCO
Three-dimensional
  • 3D J-modulated HSQC
  • 3D HNCA gradient enhanced
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