NMR paper NMR chemical shift prediction and structural elucidation of linker-containing oligo- and polysaccharides using the computer program CASPER

		BioNMR > Educational resources > Journal club
[NMR paper] NMR chemical shift prediction and structural elucidation of linker-containing oligo- and polysaccharides using the computer program CASPER

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

09-22-2023, 10:23 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

NMR chemical shift prediction and structural elucidation of linker-containing oligo- and polysaccharides using the computer program CASPER

NMR chemical shift prediction and structural elucidation of linker-containing oligo- and polysaccharides using the computer program CASPER

Carbohydrate structures containing alkyl groups as aglycones are useful for investigating enzyme activity and glycan-protein interactions. Moreover, linker-containing oligosaccharides with a spacer group are commonly used to print glycan microarrays or to prepare protein-conjugates as vaccine candidates. The structural accuracy of these synthesized glycans are essential for interpretation of results from biological experiments in which the compounds have been used and NMR spectroscopy can...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
NMR chemical shift analysis decodes olefin oligo- and polymerization activity of d0 group 4 metal complexes [Chemistry] NMR chemical shift analysis decodes olefin oligo- and polymerization activity of d0 group 4 metal complexes Christopher P. Gordon, Satoru Shirase, Keishi Yamamoto, Richard A. Andersen, Odile Eisenstein, Christophe Coperet... Date: 2018-06-26 d0 metal-alkyl complexes (M = Ti, Zr, and Hf) show specific activity and selectivity in olefin polymerization and oligomerization depending on their ligand set and charge. Here, we show by a combined experimental and computational study that the 13C NMR chemical shift tensors of the ?-carbon of metal alkyls that... Read More PNAS: Number: 26	nmrlearner	Journal club	0	06-27-2018 01:51 AM
[NMR paper] Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N. Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N. Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N. Methods Mol Biol. 2015;1260:17-32 Authors: Shen Y, Bax A Abstract Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors, and the artificial neural network based TALOS-N program has been trained to...	nmrlearner	Journal club	0	12-17-2014 09:43 PM
[NMR paper] NightShift: NMR Shift Inference by General Hybrid Model Training - a Framework for NMR Chemical Shift Prediction. NightShift: NMR Shift Inference by General Hybrid Model Training - a Framework for NMR Chemical Shift Prediction. Related Articles NightShift: NMR Shift Inference by General Hybrid Model Training - a Framework for NMR Chemical Shift Prediction. BMC Bioinformatics. 2013 Mar 16;14(1):98 Authors: Dehof AK, Loew S, Lenhof HP, Hildebrandt A Abstract NMR chemical shift prediction plays an important role in various applications in computational biology. Among others, structure determination, structure optimization, and the scoring of docking...	nmrlearner	Journal club	0	03-19-2013 01:22 PM
SHIFTX2: Chemical Shift Prediction SHIFTX2 website SHIFTX2 is capable of rapidly and accurately calculating diamagnetic 1H, 13C and 15N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3× smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more), is significantly faster (up to 8.5×) and capable of calculating a wider variety of backbone and side chain...	gwnmr	NMR software	0	01-10-2012 06:13 PM
SHIFTX2: significantly improved protein chemical shift prediction SHIFTX2: significantly improved protein chemical shift prediction Abstract A new computer program, called SHIFTX2, is described which is capable of rapidly and accurately calculating diamagnetic 1H, 13C and 15N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3Ã? smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more),...	nmrlearner	Journal club	0	04-01-2011 09:31 PM
[NMR paper] CAMRA: chemical shift based computer aided protein NMR assignments. CAMRA: chemical shift based computer aided protein NMR assignments. Related Articles CAMRA: chemical shift based computer aided protein NMR assignments. J Biomol NMR. 1998 Oct;12(3):395-405 Authors: Gronwald W, Willard L, Jellard T, Boyko RF, Rajarathnam K, Wishart DS, Sönnichsen FD, Sykes BD A suite of programs called CAMRA (Computer Aided Magnetic Resonance Assignment) has been developed for computer assisted residue-specific assignments of proteins. CAMRA consists of three units: ORB, CAPTURE and PROCESS. ORB predicts NMR chemical shifts...	nmrlearner	Journal club	0	11-17-2010 11:15 PM
Protein secondary structure prediction using NMR chemical shift data. Protein secondary structure prediction using NMR chemical shift data. Related Articles Protein secondary structure prediction using NMR chemical shift data. J Bioinform Comput Biol. 2010 Oct;8(5):867-84 Authors: Zhao Y, Alipanahi B, Li SC, Li M Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b)...	nmrlearner	Journal club	0	10-29-2010 07:05 PM
Chemical shift prediction in random coil peptides Please check this program and let me know if it does work for your random coil peptides. http://bloch.anu.edu.au/cgi-bin/shiftpred/shiftpred.cgi Thank you, Bogdan Bancia bbancia@yahoo.com	bbancia	NMR software	2	04-13-2007 03:54 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