NMR paper NMR Molecular Replacement Provides New Insights into Binding Modes to Bromodomains of BRD4 and TRIM24

		BioNMR > Educational resources > Journal club
[NMR paper] NMR Molecular Replacement Provides New Insights into Binding Modes to Bromodomains of BRD4 and TRIM24

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

04-01-2022, 03:04 AM

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 Molecular Replacement Provides New Insights into Binding Modes to Bromodomains of BRD4 and TRIM24

NMR Molecular Replacement Provides New Insights into Binding Modes to Bromodomains of BRD4 and TRIM24

Structure-based drug discovery (SBDD) largely relies on structural information from X-ray crystallography because traditional NMR structure calculation methods are too time consuming to be aligned with typical drug discovery timelines. The recently developed NMR molecular replacement (NMR²) method dramatically reduces the time needed to generate ligand-protein complex structures using published structures (apo or holo) of the target protein and treating all observed NOEs as ambiguous restraints,...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Structural Characterization of the RNA-Binding Protein SERBP1 Reveals Intrinsic Disorder and Atypical RNA Binding Modes - DocWire News Structural Characterization of the RNA-Binding Protein SERBP1 Reveals Intrinsic Disorder and Atypical RNA Binding Modes - DocWire News Structural Characterization of the RNA-Binding Protein SERBP1 Reveals Intrinsic Disorder and Atypical RNA Binding Modes DocWire News Read here	nmrlearner	Online News	0	10-15-2021 05:53 PM
Structural Characterization of the RNA-Binding Protein SERBP1 Reveals Intrinsic Disorder and Atypical RNA Binding Modes - DocWire News Structural Characterization of the RNA-Binding Protein SERBP1 Reveals Intrinsic Disorder and Atypical RNA Binding Modes - DocWire News Structural Characterization of the RNA-Binding Protein SERBP1 Reveals Intrinsic Disorder and Atypical RNA Binding Modes DocWire News Read here	nmrlearner	Online News	0	10-12-2021 02:52 PM
[NMR paper] Binding mode of AIF(370-394) peptide to CypA: insights from NMR, label-free and molecular docking studies. Binding mode of AIF(370-394) peptide to CypA: insights from NMR, label-free and molecular docking studies. Related Articles Binding mode of AIF(370-394) peptide to CypA: insights from NMR, label-free and molecular docking studies. Biochem J. 2018 Jun 11;: Authors: Farina B, Sturlese M, Mascanzoni F, Caporale A, Monti A, Di Sorbo G, Fattorusso R, Ruvo M, Doti N Abstract The complex formation between the proteins Apoptosis Inducing Factor (AIF) and Cyclophilin A (CypA) following oxidative stress in neuronal cells has been suggested...	nmrlearner	Journal club	0	06-13-2018 05:09 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] 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	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
[NMR paper] A combined STD-NMR/molecular modeling protocol for predicting the binding modes of th A combined STD-NMR/molecular modeling protocol for predicting the binding modes of the glycosidase inhibitors kifunensine and salacinol to Golgi alpha-mannosidase II. Related Articles A combined STD-NMR/molecular modeling protocol for predicting the binding modes of the glycosidase inhibitors kifunensine and salacinol to Golgi alpha-mannosidase II. Biochemistry. 2005 May 10;44(18):6729-37 Authors: Wen X, Yuan Y, Kuntz DA, Rose DR, Pinto BM A combined STD-NMR/molecular modeling protocol to probe the binding modes of the glycosidase inhibitors...	nmrlearner	Journal club	0	11-25-2010 08:21 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