UncoveringNonconventional and Conventional HydrogenBonds in Oligosaccharides through NMR Experiments and Molecular Modeling:Application to Sialyl Lewis-X

		BioNMR > Educational resources > Journal club
UncoveringNonconventional and Conventional HydrogenBonds in Oligosaccharides through NMR Experiments and Molecular Modeling:Application to Sialyl Lewis-X

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

10-16-2015, 12:49 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,791

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

UncoveringNonconventional and Conventional HydrogenBonds in Oligosaccharides through NMR Experiments and Molecular Modeling:Application to Sialyl Lewis-X

UncoveringNonconventional and Conventional HydrogenBonds in Oligosaccharides through NMR Experiments and Molecular Modeling:Application to Sialyl Lewis-X

Marcos D. Battistel, Hugo F. Azurmendi, Martin Frank and Daro?n I. Freedberg

Journal of the American Chemical Society
DOI: 10.1021/jacs.5b03824

Source: Journal of the American Chemical Society

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation. Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation. Adv Exp Med Biol. 2015;842:217-30 Authors: Zhang Y, Yamaguchi T, Satoh T, Yagi-Utsumi M, Kamiya Y,...	nmrlearner	Journal club	0	05-02-2015 09:41 PM
[NMR paper] Application of Reductive 13C-Methylation of Lysines to Enhance the Sensitivity of Conventional NMR Methods. Application of Reductive 13C-Methylation of Lysines to Enhance the Sensitivity of Conventional NMR Methods. Application of Reductive 13C-Methylation of Lysines to Enhance the Sensitivity of Conventional NMR Methods. Molecules. 2013;18(6):7103-19 Authors: Chavan TS, Abraham S, Gaponenko V Abstract NMR is commonly used to investigate macromolecular interactions. However, sensitivity problems hamper its use for studying such interactions at low physiologically relevant concentrations. At high concentrations, proteins or peptides tend to...	nmrlearner	Journal club	0	06-20-2013 10:08 AM
Synthesis and Molecular Recognition Studies of the HNK-1 Trisaccharide and Related Oligosaccharides. The Specificity of Monoclonal Anti-HNK-1 Antibodies as Assessed by Surface Plasmon Resonance and STD NMR Synthesis and Molecular Recognition Studies of the HNK-1 Trisaccharide and Related Oligosaccharides. The Specificity of Monoclonal Anti-HNK-1 Antibodies as Assessed by Surface Plasmon Resonance and STD NMR Yury E. Tsvetkov, Monika Burg-Roderfeld, Gabriele Loers, Ana Arda?, Elena V. Sukhova, Elena A. Khatuntseva, Alexey A. Grachev, Alexander O. Chizhov, Hans-Christian Siebert, Melitta Schachner, Jesu?s Jime?nez-Barbero and Nikolay E. Nifantiev ...	nmrlearner	Journal club	0	12-20-2011 04:09 AM
[NMR paper] The application of x-ray, NMR, and molecular modeling in the design of MMP inhibitors The application of x-ray, NMR, and molecular modeling in the design of MMP inhibitors. Related Articles The application of x-ray, NMR, and molecular modeling in the design of MMP inhibitors. Curr Top Med Chem. 2004;4(12):1311-27 Authors: Rush TS, Powers R The following review discusses the successful application of X-ray, NMR, and molecular modeling in the design of potent and selective inhibitors of matrix metalloproteinases (MMPs) and TNFalpha-converting enzyme (TACE) from Wyeth. The importance of protein and ligand mobility as it impacts...	nmrlearner	Journal club	0	11-24-2010 09:25 PM
[NMR paper] Epitope mapping of sialyl Lewis(x) bound to E-selectin using saturation transfer diff Epitope mapping of sialyl Lewis(x) bound to E-selectin using saturation transfer difference NMR experiments. Related Articles Epitope mapping of sialyl Lewis(x) bound to E-selectin using saturation transfer difference NMR experiments. Glycobiology. 2003 Jun;13(6):435-43 Authors: Rinnbauer M, Ernst B, Wagner B, Magnani J, Benie AJ, Peters T A complex between sialyl Lewisx (alpha-D-Neu5Ac-- beta-D-Gal---beta-D-GlcNAc-O-8 COOMe) and E-selectin was studied using saturation transfer difference (STD) nuclear magnetic resonance (NMR) experiments....	nmrlearner	Journal club	0	11-24-2010 09:01 PM
[NMR paper] Structure and dynamics of oligosaccharides: NMR and modeling studies. Structure and dynamics of oligosaccharides: NMR and modeling studies. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Structure and dynamics of oligosaccharides: NMR and modeling studies. Curr Opin Struct Biol. 1996 Oct;6(5):710-20 Authors: Peters T, Pinto BM Recent advances in the conformational analysis of oligosaccharides have focused on protein-bound oligosaccharides, glycopeptides, and glycoproteins, as well as on the conformational dynamics about glycosidic...	nmrlearner	Journal club	0	08-22-2010 02:20 PM
Molecular Modeling Molecular ModelingWHAT If Calculation AutoStructure: Automated Determination of Protein Structures from NMR Data GenCons Hyper Queen Analysis Database of Macromolecular Movements with Associated Tools for Geometric Analysis PDBStat Dynamics	ale51	BioNMR Wiki	2	08-23-2006 04:46 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