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NMR processing:
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Side-chains:
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NOEs:
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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:
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Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
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RPF scores
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Chemical shifts:
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CheShift2
Vasco
iCing
RDCs:
DC
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Pseudocontact shifts:
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Protein geomtery:
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PROSESS
What-If
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PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
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STAN
Ramachandran Plot
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ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
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V-NMR
Flexibility from structure:
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Methyl S2
B-factor
Molecular dynamics:
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Chemical shifts prediction:
From structure:
Shiftx2
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CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
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Camcoil
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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
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camGroEL
Zyggregator
Isotope labeling:
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Solid-state NMR:
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  #1  
Old 12-24-2005, 12:14 PM
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Default Answered: How do you use NMR to tell the conformation of a molecule?

I'm looking at an NMR and its chemical shifts and J-coupling values and I need some help on using J-coupling to tell conformation. Anyone have some tips, pointers, anything?nemeczek, thankyou for your answer. I am aware of the karplus equation and finding the dihedral angle. I'm not entirely sure what to do with that information though. Can you give me a few pointers?Ensur, thankyou for trying to help. I know what my compound is supposed to be and I know the basics of reading NMR. I'm working on 1H NMR by the way. I need to know how the dihedral angle tells you the specific conformation though.
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Best Answer - Posted by nemeczek
Find the Karplus curve which describes the dependence of J on the value of the H-C-C-H dihedral angle.First of all, you need to be sure that the rate of interconvertion between the conformations is slow at the NMR time scale. If it is too fast, you will observe the average conformation by NMR. It can still provide you some information as to the population distribution between the conformations, though.If your molecule contains a six- or five-membered ring, the dihedral angle between H(axial)-C-C-H(axial) is obviously different than for its equatorial-equatorial counterpart. It would manifest itself in a different value of J.

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Old 12-24-2005, 12:14 PM
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Default How do you use NMR to tell the conformation of a molecule?

Find the Karplus curve which describes the dependence of J on the value of the H-C-C-H dihedral angle.First of all, you need to be sure that the rate of interconvertion between the conformations is slow at the NMR time scale. If it is too fast, you will observe the average conformation by NMR. It can still provide you some information as to the population distribution between the conformations, though.If your molecule contains a six- or five-membered ring, the dihedral angle between H(axial)-C-C-H(axial) is obviously different than for its equatorial-equatorial counterpart. It would manifest itself in a different value of J.
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Old 12-24-2005, 09:26 PM
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Default How do you use NMR to tell the conformation of a molecule?

Which NMR are you looking at? C13 or H1?I'm most familiar with H1. What I do is just read each signal at a time. First, if I'm given the compund, I'll calculate the index of hydrogen deficiency to tell me if I have any crazy double or triple bonds or aromatic compounds.Then I'll count how many unique signals I have. And then I'll take it one at a time. If one of the signals is a 3H doublet, I can draw a C with 3 H's on it, and a second C connected to that C, with 1 H on it since the reading is a doublet (remember coupling).I wish I could help you out with 13C but, don't quite remember it as well.As for chemical shifts, http://wwwchem.csustan.edu/Tutorials/NMRTABLE.HTM will tell you what kind of substrates produce which chemical shifts. Best thing to do is just memorize them.

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