NMR paper AlphaFold2 as a replacement for solution NMR structure determination of small proteins: Not so fast!

		BioNMR > Educational resources > Journal club
[NMR paper] AlphaFold2 as a replacement for solution NMR structure determination of small proteins: Not so fast!

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

06-26-2024, 01:21 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

AlphaFold2 as a replacement for solution NMR structure determination of small proteins: Not so fast!

AlphaFold2 as a replacement for solution NMR structure determination of small proteins: Not so fast!

The determination of a protein's structure is often a first step towards the development of a mechanistic understanding of its function. Considerable advances in computational protein structure prediction have been made in recent years, with AlphaFold2 (AF2) emerging as the primary tool used by researchers for this purpose. While AF2 generally predicts accurate structures of folded proteins, we present here a case where AF2 incorrectly predicts the structure of a small, folded and compact...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Optimization of the methods for small peptide solution structure determination by NMR spectroscopy From Mendeley Biomolecular NMR group: Optimization of the methods for small peptide solution structure determination by NMR spectroscopy Mol Biol (Mosk) (2010). Volume: 44, Issue: 6. Pages: 1075-1085. A N Istrate, A B Mantsyzov, S A Kozin, V I Pol'shakov et al. NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints...	nmrlearner	Journal club	0	01-29-2016 12:59 PM
[NMR paper] Optimization of the methods for small peptide solution structure determination by NMR spectroscopy From Mendeley Biomolecular NMR group: Optimization of the methods for small peptide solution structure determination by NMR spectroscopy Mol Biol (Mosk) (2010). Volume: 44, Issue: 6. Pages: 1075-1085. A N Istrate, A B Mantsyzov, S A Kozin, V I Pol'shakov et al. NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints...	nmrlearner	Journal club	0	09-29-2015 02:39 PM
[NMR paper] Optimization of the methods for small peptide solution structure determination by NMR spectroscopy From Mendeley Biomolecular NMR group: Optimization of the methods for small peptide solution structure determination by NMR spectroscopy Mol Biol (Mosk) (2010). Volume: 44, Issue: 6. Pages: 1075-1085. A N Istrate, A B Mantsyzov, S A Kozin, V I Pol'shakov et al. NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints...	nmrlearner	Journal club	0	10-17-2013 12:49 PM
[NMR paper] Optimization of the methods for small peptide solution structure determination by NMR spectroscopy From Mendeley Biomolecular NMR group: Optimization of the methods for small peptide solution structure determination by NMR spectroscopy Mol Biol (Mosk) (2010). Volume: 44, Issue: 6. Pages: 1075-1085. A N Istrate, A B Mantsyzov, S A Kozin, V I Pol'shakov et al. NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints...	nmrlearner	Journal club	0	01-09-2013 04:20 PM
[NMR paper] Optimization of the methods for small peptide solution structure determination by NMR spectroscopy From Mendeley Biomolecular NMR group: Optimization of the methods for small peptide solution structure determination by NMR spectroscopy Mol Biol (Mosk) (2010). Volume: 44, Issue: 6. Pages: 1075-1085. A N Istrate, A B Mantsyzov, S A Kozin, V I Pol'shakov et al. NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints...	nmrlearner	Journal club	0	11-15-2012 06:46 PM
[NMR paper] Optimization of the methods for small peptide solution structure determination by NMR spectroscopy From Mendeley Biomolecular NMR group: Optimization of the methods for small peptide solution structure determination by NMR spectroscopy Mol Biol (Mosk) (2010). Volume: 44, Issue: 6. Pages: 1075-1085. A N Istrate, A B Mantsyzov, S A Kozin, V I Pol'shakov et al. NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints...	nmrlearner	Journal club	0	10-12-2012 09:58 AM
[NMR paper] Optimization of the methods for small peptide solution structure determination by NMR spectroscopy From Mendeley Biomolecular NMR group: Optimization of the methods for small peptide solution structure determination by NMR spectroscopy Mol Biol (Mosk) (2010). Volume: 44, Issue: 6. Pages: 1075-1085. A N Istrate, A B Mantsyzov, S A Kozin, V I Pol'shakov et al. NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints...	nmrlearner	Journal club	0	08-24-2012 08:01 PM
[Optimization of the methods for small peptide solution structure determination by NMR spectroscopy]. . . Mol Biol (Mosk). 2010 Nov-Dec;44(6):1075-85 Authors: NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints from NMR spectra. At the same time, short charged peptides play an important role in a number of biological processes, in particular in pathogenesis of neurodegenerative...	nmrlearner	Journal club	0	02-05-2011 05:28 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