Integrated Computational Approach to the Analysis of NMR Relaxation in Proteins: Application to ps-ns Main Chain (15)N-(1)H and Global Dynamics of the Rho GTPase Binding Domain of Plexin-B1.

		BioNMR > Educational resources > Journal club
Integrated Computational Approach to the Analysis of NMR Relaxation in Proteins: Application to ps-ns Main Chain (15)N-(1)H and Global Dynamics of the Rho GTPase Binding Domain of Plexin-B1.

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

12-15-2010, 12:03 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,697

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

Integrated Computational Approach to the Analysis of NMR Relaxation in Proteins: Application to ps-ns Main Chain (15)N-(1)H and Global Dynamics of the Rho GTPase Binding Domain of Plexin-B1.

Integrated Computational Approach to the Analysis of NMR Relaxation in Proteins: Application to ps-ns Main Chain (15)N-(1)H and Global Dynamics of the Rho GTPase Binding Domain of Plexin-B1.

Integrated Computational Approach to the Analysis of NMR Relaxation in Proteins: Application to ps-ns Main Chain (15)N-(1)H and Global Dynamics of the Rho GTPase Binding Domain of Plexin-B1.

J Phys Chem B. 2010 Dec 10;

Authors: Zerbetto M, Buck M, Meirovitch E, Polimeno A

PMID: 21142011 [PubMed - as supplied by publisher]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Insights into the interaction of discodermolide and docetaxel with tubulin. Mapping the binding sites of microtubule-stabilizing agents by using an integrated NMR and computational approach. Insights into the interaction of discodermolide and docetaxel with tubulin. Mapping the binding sites of microtubule-stabilizing agents by using an integrated NMR and computational approach. Insights into the interaction of discodermolide and docetaxel with tubulin. Mapping the binding sites of microtubule-stabilizing agents by using an integrated NMR and computational approach. ACS Chem Biol. 2011 May 3; Authors: Canales A, R Salarichs J, Trigili C, Nieto L, Coderch C, Andreu JM, Paterson I, Jimenez-Barbero J, Díaz Pereira JF The binding...	nmrlearner	Journal club	0	05-06-2011 02:00 AM
Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins Abstract Extensive resonance overlap exacerbates assignment of intrinsically disordered proteins (IDPs). This issue can be circumvented by utilizing 15N, 13Câ?² and 1HN spins, where the chemical shift dispersion is mainly dictated by the characteristics of consecutive amino acid residues. Especially 15N and 13Câ?² spins offer superior chemical shift dispersion in comparison to 13CÎ± and 13CÎ² spins. However, HN-detected experiments...	nmrlearner	Journal club	0	01-29-2011 05:31 AM
[NMR paper] NMR investigation of main-chain dynamics of the H80E mutant of bovine neurophysin-I: demonstration of dimerization-induced changes at the hormone-binding site. NMR investigation of main-chain dynamics of the H80E mutant of bovine neurophysin-I: demonstration of dimerization-induced changes at the hormone-binding site. Related Articles NMR investigation of main-chain dynamics of the H80E mutant of bovine neurophysin-I: demonstration of dimerization-induced changes at the hormone-binding site. Biochemistry. 2005 Sep 6;44(35):11766-76 Authors: Naik MT, Lee H, Bracken C, Breslow E Neurophysins are hormone-binding proteins composed of two partially homologous domains. Ligand-binding (localized to the...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] Changes in calmodulin main-chain dynamics upon ligand binding revealed by cross-corre Changes in calmodulin main-chain dynamics upon ligand binding revealed by cross-correlated NMR relaxation measurements. Related Articles Changes in calmodulin main-chain dynamics upon ligand binding revealed by cross-correlated NMR relaxation measurements. J Am Chem Soc. 2005 Jan 26;127(3):828-9 Authors: Wang T, Frederick KK, Igumenova TI, Wand AJ, Zuiderweg ER The fast dynamics of protein backbones are often investigated by nuclear magnetic relaxation experiments that report on the degree of spatial restriction of the amide bond vector. By...	nmrlearner	Journal club	0	11-24-2010 11:14 PM
[NMR paper] Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studi Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2. Related Articles Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2. Biochemistry. 2001 Jun 5;40(22):6559-69 Authors: Flynn PF, Bieber Urbauer RJ, Zhang H, Lee AL, Wand AJ A detailed characterization of the main chain and side chain dynamics in R. capsulatus ferrocytochrome c(2) derived from (2)H NMR relaxation of methyl group resonances is...	nmrlearner	Journal club	0	11-19-2010 08:32 PM
[NMR paper] A simple approach to analyzing protein side-chain dynamics from 13C NMR relaxation da A simple approach to analyzing protein side-chain dynamics from 13C NMR relaxation data. Related Articles A simple approach to analyzing protein side-chain dynamics from 13C NMR relaxation data. J Magn Reson. 1998 Feb;130(2):329-34 Authors: Daragan VA, Mayo KH A simple approach to deriving motional dynamics information of protein and peptide side chains by using 13C NMR relaxation data is presented. By using linear approximation of internal rotational correlation functions, simple equations for relating side-chain conformation, bond rotational...	nmrlearner	Journal club	0	11-17-2010 11:06 PM
[NMR paper] Main-chain dynamics of a partially folded protein: 15N NMR relaxation measurements of Main-chain dynamics of a partially folded protein: 15N NMR relaxation measurements of hen egg white lysozyme denatured in trifluoroethanol. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Main-chain dynamics of a partially folded protein: 15N NMR relaxation measurements of hen egg white lysozyme denatured in trifluoroethanol. J Mol Biol. 1996 Apr 5;257(3):669-83 Authors: Buck M, Schwalbe H, Dobson CM 15N NMR relaxation measurements have been used to study the dynamic...	nmrlearner	Journal club	0	08-22-2010 02:27 PM
[NMR paper] Analysis of main chain torsion angles in proteins: prediction of NMR coupling constan Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations. J Mol Biol. 1996 Jan 26;255(3):494-506 Authors: Smith LJ, Bolin KA, Schwalbe H, MacArthur MW, Thornton JM, Dobson CM Using a data base of 85 high resolution protein...	nmrlearner	Journal club	0	08-22-2010 02:27 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