Proteinâ??ligand structure determination with the NMR molecular replacement tool, N MR 2

		BioNMR > Educational resources > Journal club
Proteinâ??ligand structure determination with the NMR molecular replacement tool, N MR 2

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

07-04-2020, 03:45 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

Proteinâ??ligand structure determination with the NMR molecular replacement tool, N MR 2

Proteinâ??ligand structure determination with the NMR molecular replacement tool, N MR 2

Abstract

We recently reported on a new method called NMR Molecular Replacement that efficiently derives the structure of a proteinâ??ligand complex at the interaction site. The method was successfully applied to high and low affinity complexes covering ligands from peptides to small molecules. The algorithm used in the NMR Molecular Replacement program has until now not beenÂ*described in detail. Here, we present a complete description of the NMR Molecular Replacement implementation as well as several new features that further reduce the time required for structure elucidation.

Source: Journal of Biomolecular NMR

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Trimethylsilyl tag for probing proteinâ??ligand interactions by NMR Trimethylsilyl tag for probing proteinâ??ligand interactions by NMR Abstract Proteinâ??ligand titrations can readily be monitored with a trimethylsilyl (TMS) tag. Owing to the intensity, narrow line shape and unique chemical shift of a TMS group, dissociation constants can be determined from straightforward 1D 1H-NMR spectra not only in the fast but also in the slow exchange limit. The tag is easily attached to cysteine residues and a sensitive reporter of ligand binding also at sites where it does not interfere with ligand binding or catalytic...	nmrlearner	Journal club	0	03-21-2018 04:04 PM
Determination of ligand binding modes in weak proteinâ??ligand complexes using sparse NMR data Determination of ligand binding modes in weak proteinâ??ligand complexes using sparse NMR data Abstract We describe a general approach to determine the binding pose of small molecules in weakly bound proteinâ??ligand complexes by deriving distance constraints between the ligand and methyl groups from all methyl-containing residues of the protein. We demonstrate that using a single sample, which can be prepared without the use of expensive precursors, it is possible to generate high-resolution data rapidly and obtain the resonance assignments of...	nmrlearner	Journal club	0	11-19-2016 08:35 PM
Proteinâ??ligand structure guided by backbone and side-chain proton chemical shift perturbations Proteinâ??ligand structure guided by backbone and side-chain proton chemical shift perturbations Abstract The fragment-based drug design approach consists of screening libraries of fragment-like ligands, to identify hits that typically bind the protein target with weak affinity ( \(100\,\upmu \hbox {M}\) â??5Â*mM). The determination of the proteinâ??fragment complex 3D structure constitutes a crucial step for uncovering the key interactions responsible for...	nmrlearner	Journal club	0	09-26-2014 01:03 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] 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
Convenient method for resolving degeneracies due to symmetry of the magnetic susceptibility tensor and its application to pseudo contact shift-based proteinâ??protein complex structure determination Convenient method for resolving degeneracies due to symmetry of the magnetic susceptibility tensor and its application to pseudo contact shift-based proteinâ??protein complex structure determination Abstract Pseudo contact shifts (PCSs) induced by paramagnetic lanthanide ions fixed in a protein frame provide long-range distance and angular information, and are valuable for the structure determination of proteinâ??protein and proteinâ??ligand complexes. We have been developing a lanthanide-binding peptide tag (hereafter LBT) anchored at two points via a peptide bond and a disulfide ...	nmrlearner	Journal club	0	04-12-2012 06:12 AM
PCS-based structure determination of proteinâ??protein complexes Abstract A simple and fast nuclear magnetic resonance method for docking proteins using pseudo-contact shift (PCS) and 1HN/15N chemical shift perturbation is presented. PCS is induced by a paramagnetic lanthanide ion that is attached to a target protein using a lanthanide binding peptide tag anchored at two points. PCS provides long-range (~40 Ã?) distance and angular restraints between the lanthanide ion and the observed nuclei, while the 1HN/15N chemical shift perturbation data provide loose contact-surface information. The usefulness of this method was demonstrated through the structure...	nmrlearner	Journal club	0	08-14-2010 04:19 AM

« 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