Question from NMRWiki Q&A forum simulating 2D-NOESY spectrum from structural model

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[Question from NMRWiki Q&A forum] simulating 2D-NOESY spectrum from structural model

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NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

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05-06-2014, 01:57 AM

nmrlearner

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simulating 2D-NOESY spectrum from structural model

simulating 2D-NOESY spectrum from structural model

Hello everyoneOur research group planning to study metal-ion induced structural transition using NMR. We are new to this field. Before doing the experiment,we want to do some groundwork. Hence we have an idea of simulating 2D NOESY spectrum of two structural forms of DNA deposited in PDB without any experimental NOE data and curious to know how the spectrum look like. We found out two programs relevant to our idea such as FIRM and CORMA. We started with FIRM because CORMA was a licensed one.Since we are mostly using GNU linux system, FIRM was unable to compile as it was written exclusively for SGI Irix and SUN sparc. Can anyone suggest ways or programs compatible to GNUlinux for calculating NOE distances from coordinates thereby simulate 2D spectrum? Every suggestion on this regard would be highly appreciated. Thanks in advance.

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