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

		BioNMR > NMR community > News from other NMR forums
[Question from NMRWiki Q&A forum] simulating 2D-NOESY spectrum from structural model

Webservers

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:

Thread Tools

Search this Thread

Rate Thread

Display Modes

05-06-2014, 01:57 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,778

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

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.

Check if somebody has answered this question on NMRWiki QA forum

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Peakr: Simulating solid-state NMR spectra of proteins. Peakr: Simulating solid-state NMR spectra of proteins. Related Articles Peakr: Simulating solid-state NMR spectra of proteins. Bioinformatics. 2013 Mar 14; Authors: Schneider R, Odronitz F, Hammesfahr B, Hellkamp M, Kollmar M Abstract MOTIVATION: When analyzing solid-state NMR spectra of proteins, assignment of resonances to nuclei and derivation of restraints for 3D structure calculations are challenging and time-consuming processes. Simulated spectra that have been calculated based on, e.g., chemical shift predictions and structural...	nmrlearner	Journal club	0	03-16-2013 03:18 PM
How to interpret a NOESY NMR spectrum How to interpret a NOESY NMR spectrum http://i.ytimg.com/vi/BbL-rp10jaE/default.jpg How to interpret a NOESY NMR spectrum In this tutorial we look at how to interpret a NOESY NMR spectrum using a tripeptide as an example. 2D homogeneous NOE spectroscopy (NOESY) is a widely used ... From:chemtubeuk Views:2521 http://gdata.youtube.com/static/images/icn_star_full_11x11.gif http://gdata.youtube.com/static/images/icn_star_full_11x11.gif http://gdata.youtube.com/static/images/icn_star_full_11x11.gif http://gdata.youtube.com/static/images/icn_star_full_11x11.gif...	nmrlearner	NMR educational videos	0	03-07-2013 05:38 AM
[Question from NMRWiki Q&A forum] Auto peak picking of N15Edit NOESY and C13 Edit NOESY spectrum Auto peak picking of N15Edit NOESY and C13 Edit NOESY spectrum Dear friends, I am in process of doing structure calculation of a dimeric protein. The problem I faced is regarding the assignment of N15Edit NOESY and C13 Edit NOESY spectrum.I have already processed the fid data and converted to sparky ucsf format. Is there options available in sparky for auto peak picking, integration and assignment of my NOESY spectrum? And second query is regarding the generation of input files for structure calculation. In our Lab we are using ARIA 2.1 software for structure calculation? Is there any...	nmrlearner	News from other NMR forums	0	12-14-2011 07:14 PM
[NMRpipe Yahoo group] Re: A sample 4D HCCH Noesy spectrum Re: A sample 4D HCCH Noesy spectrum This is an example for an HN-Methyl 4D I have, not exactly the same, but perhaps useful to see anyway ... the processing scheme is a very basic one ... More...	NMRpipe Yahoo group news	News from other NMR forums	0	12-13-2011 02:46 AM
[NMRpipe Yahoo group] Re: A sample 4D HCCH Noesy spectrum Re: A sample 4D HCCH Noesy spectrum Hi Have you tried the example from NMRDraw macro editor? (under process 4D) I believe nothing is special in term of processing data. Phasing, sweep width, and More...	NMRpipe Yahoo group news	News from other NMR forums	0	12-10-2011 02:38 AM
[NMRpipe Yahoo group] A sample 4D HCCH Noesy spectrum A sample 4D HCCH Noesy spectrum Hello, I'm struggling to process a 4D methyl noesy spectrum collected on a Bruker and I was wondering if anyone knows where I could find an example ser file More...	NMRpipe Yahoo group news	News from other NMR forums	0	12-10-2011 02:38 AM
Transferred NOESY NMR studies of biotin mimetic peptide (FSHPQNT) bound to streptavidin: A structural model for studies of peptide-protein interactions. Transferred NOESY NMR studies of biotin mimetic peptide (FSHPQNT) bound to streptavidin: A structural model for studies of peptide-protein interactions. Transferred NOESY NMR studies of biotin mimetic peptide (FSHPQNT) bound to streptavidin: A structural model for studies of peptide-protein interactions. Chem Biol Drug Des. 2011 Feb 5; Authors: Gizachew D, Dratz E Protein-protein interactions control signaling, specific adhesion and many other biological functions. The three dimensional structures of the interfaces and bound ligand can be...	nmrlearner	Journal club	0	02-08-2011 06:28 PM
[NMR paper] Heteronuclear NMR and soft docking: an experimental approach for a structural model o Heteronuclear NMR and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex. Related Articles Heteronuclear NMR and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex. Biochemistry. 2000 Mar 14;39(10):2530-7 Authors: Morelli X, Dolla A, Czjzek M, Palma PN, Blasco F, Krippahl L, Moura JJ, Guerlesquin F The combination of docking algorithms with NMR data has been developed extensively for the studies of protein-ligand interactions. However, to...	nmrlearner	Journal club	0	11-18-2010 09:15 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off