NMR paper Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology

		BioNMR > Educational resources > Journal club
[NMR paper] Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology

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

03-01-2024, 10:10 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

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

Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology

Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology

The validity of protein structures and interactions, whether determined under ideal laboratory conditions or predicted by AI tools such as Alphafold2, to precisely reflect those found in living cells remains to be examined. Moreover, understanding the changes in protein structures and interactions in response to stimuli within living cells, under both normal and disease conditions, is key to grasping proteins' functionality and cellular processes. Nevertheless, achieving high-resolution...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Biomolecular NMR in the AI-assisted structural biology era: Old tricks and new opportunities Biomolecular NMR in the AI-assisted structural biology era: Old tricks and new opportunities Over the last 40 years nuclear magnetic resonance (NMR) spectroscopy has established itself as one of the most versatile techniques for the characterization of biomolecules, especially proteins. Given the molecular size limitations of NMR together with recent advances in cryo-electron microscopy and artificial intelligence-assisted protein structure prediction, the bright future of NMR in structural biology has been put into question. In this mini review we argue the contrary. We discuss the... ...	nmrlearner	Journal club	0	08-13-2023 11:17 AM
Opportunities and Challenges for EIK's in DNP NMR Applications #DNPNMR From The DNP-NMR Blog: Opportunities and Challenges for EIK's in DNP NMR Applications #DNPNMR Rosay, Melanie, Ivan Scrgeyev, Leo Tometich, Christopher Hickey, Albert Roitman, Doug Yake, and Dave Berry. “Opportunities and Challenges for EIK’s in DNP NMR Applications.” In 2018 43rd International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz), 1–2. Nagoya: IEEE, 2018. https://doi.org/10.1109/IRMMW-THz.2018.8510328.	nmrlearner	News from NMR blogs	0	02-29-2020 09:52 PM
[NMR paper] NMR of Macromolecular Assemblies and Machines at 1 GHz and Beyond: New Transformative Opportunities for Molecular Structural Biology. NMR of Macromolecular Assemblies and Machines at 1 GHz and Beyond: New Transformative Opportunities for Molecular Structural Biology. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles NMR of Macromolecular Assemblies and Machines at 1 GHz and Beyond: New Transformative Opportunities for Molecular Structural Biology. Methods Mol Biol. 2018;1688:1-35 Authors: Quinn CM, Wang M, Polenova T Abstract As a result of profound gains in...	nmrlearner	Journal club	0	11-21-2017 10:10 PM
[NMR paper] A Unique Tool for Cellular Structural Biology: In-cell NMR. A Unique Tool for Cellular Structural Biology: In-cell NMR. Related Articles A Unique Tool for Cellular Structural Biology: In-cell NMR. J Biol Chem. 2015 Dec 16; Authors: Luchinat E, Banci L Abstract Conventional structural and chemical biology approaches are applied to macromolecules extrapolated from their native context. When doing so, important structural and functional features of macromolecules may be lost, which depend on their native network of interactions within the cell. In-cell nuclear magnetic resonance is a branch...	nmrlearner	Journal club	0	12-28-2015 12:26 AM
Structural biology Structure in the cellular context - Nature.com <img alt="" height="1" width="1"> Structural biology Structure in the cellular context Nature.com Researchers develop an approach based on solid-state nuclear magnetic resonance (NMR) to study the structure of an intrinsically disordered protein under near-native conditions. Traditionally, investigations into the molecular structure of a protein ... Structural biology Structure in the cellular context - Nature.com More...	nmrlearner	Online News	0	12-09-2015 09:03 AM
Structural biology Structure in the cellular context - Nature.com <img alt="" height="1" width="1"> Structural biology Structure in the cellular context Nature.com Researchers develop an approach based on solid-state nuclear magnetic resonance (NMR) to study the structure of an intrinsically disordered protein under near-native conditions. Traditionally, investigations into the molecular structure of a protein ... Structural biology Structure in the cellular context - Nature.com More...	nmrlearner	Online News	0	12-01-2015 11:22 PM
[NMR images] To address the challenges in membrane protein structural biology http://www.columbuslabs.org/wp-content/uploads/2010/05/fig3a_new.png 22/04/2014 3:22:09 AM GMT To address the challenges in membrane protein structural biology More...	nmrlearner	NMR pictures	0	04-22-2014 03:21 AM
Radiation Damping in Modern NMR Experiments: Progress and Challenges Radiation Damping in Modern NMR Experiments: Progress and Challenges Publication year: 2012 Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br> V.V. Krishnan, Nagarajan Murali</br> Highlights ? Overview of radiation damping effects in biomolecular NMR experiments. ? Theory and modifications of Bloch Equations. ? Current status, artifacts, control, applications as well as constructive uses of radiation damping.</br>	nmrlearner	Journal club	0	06-15-2012 02:10 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