NMR paper Protein-fragment complex structures derived by NMR molecular replacement.

		BioNMR > Educational resources > Journal club
[NMR paper] Protein-fragment complex structures derived by NMR molecular replacement.

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:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

01-24-2021, 11:14 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,174

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

Protein-fragment complex structures derived by NMR molecular replacement.

Related Articles Protein-fragment complex structures derived by NMR molecular replacement.

RSC Med Chem. 2020 May 01;11(5):591-596

Authors: Torres F, Ghosh D, Strotz D, Chi CN, Davis B, Orts J

Abstract
Recently we have established an NMR molecular replacement method, which is capable of solving the structure of the interaction site of protein-ligand complexes in a fully automated manner. While the method was successfully applied for ligands with strong and weak binding affinities, including small molecules and peptides, its applicability on ligand fragments remains to be shown. Structures of fragment-protein complexes are more challenging for the method since fragments contain only few protons. Here we show a successful application of the NMR molecular replacement method in solving structures of complexes between three derivatives of a ligand fragment and the protein receptor PIN1. We anticipate that this approach will find a broad application in fragment-based lead discovery.

PMID: 33479661 [PubMed]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Protein-ligand structure determination with the NMR molecular replacement tool, NMR2. Protein-ligand structure determination with the NMR molecular replacement tool, NMR2. Related Articles Protein-ligand structure determination with the NMR molecular replacement tool, NMR2. J Biomol NMR. 2020 Jul 03;: Authors: Orts J, Riek R Abstract We recently reported on a new method called NMR Molecular Replacement that efficiently derives the structure of a protein-ligand complex at the interaction site. The method was successfully applied to high and low affinity complexes covering ligands from peptides to small molecules....	nmrlearner	Journal club	0	07-06-2020 10:08 AM
[NMR paper] Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts. Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts. Related Articles Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts. Proc Natl Acad Sci U S A. 2014 Sep 5; Authors: Boomsma W, Tian P, Frellsen J, Ferkinghoff-Borg J, Hamelryck T, Lindorff-Larsen K, Vendruscolo M Abstract Methods of protein structure determination based on NMR chemical shifts are becoming increasingly common. The most widely used approaches adopt the molecular...	nmrlearner	Journal club	0	09-07-2014 12:36 PM
[NMR paper] Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement. Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement. Related Articles Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement. Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2194-201 Authors: Bibby J, Keegan RM, Mayans O, Winn MD, Rigden DJ Abstract AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core...	nmrlearner	Journal club	0	11-06-2013 10:20 PM
[CNS Yahoo group] Re: Molecular replacement Re: Molecular replacement I once had a similar problem. In your case, the protein is fused so you know it is there. I suggest you get initial phases from the MBP molecular replacement More...	nmrlearner	News from other NMR forums	0	05-15-2013 03:12 PM
[CNS Yahoo group] Re: Molecular replacement Re: Molecular replacement I once had a similar problem. In your case, the protein is fused so you know it is there. I suggest you get initial phases from the MBP molecular replacement More...	nmrlearner	News from other NMR forums	0	02-11-2013 08:42 AM
[CNS Yahoo group] Molecular replacement Molecular replacement HI I have MBP fused protein. I got the x-ray data at 3.1 A resolution. I have solved the MBP structure with the MBP as a model. I can see the density More...	nmrlearner	News from other NMR forums	0	02-11-2013 08:42 AM
Improved technologies now routinely provide protein NMR structures useful for molecular replacement. Improved technologies now routinely provide protein NMR structures useful for molecular replacement. Improved technologies now routinely provide protein NMR structures useful for molecular replacement. Structure. 2011 Jun 8;19(6):757-66 Authors: Mao B, Guan R, Montelione GT Molecular replacement (MR) is widely used for addressing the phase problem in X-ray crystallography. Historically, crystallographers have had limited success using NMR structures as MR search models. Here, we report a comprehensive investigation of the utility of protein NMR...	nmrlearner	Journal club	0	06-08-2011 11:30 AM
RDC derived protein backbone resonance assignment using fragment assembly RDC derived protein backbone resonance assignment using fragment assembly Abstract Experimental residual dipolar couplings (RDCs) in combination with structural models have the potential for accelerating the protein backbone resonance assignment process because RDCs can be measured accurately and interpreted quantitatively. However, this application has been limited due to the need for very high-resolution structural templates. Here, we introduce a new approach to resonance assignment based on optimal agreement between the experimental and calculated RDCs from a structural template that...	nmrlearner	Journal club	0	12-31-2010 08:38 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