NMR paper A Novel NMR-Based Protocol to Screen Ultralow Molecular Weight Fragments

		BioNMR > Educational resources > Journal club
[NMR paper] A Novel NMR-Based Protocol to Screen Ultralow Molecular Weight Fragments

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: 23,732

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

A Novel NMR-Based Protocol to Screen Ultralow Molecular Weight Fragments

A Novel NMR-Based Protocol to Screen Ultralow Molecular Weight Fragments

Fragment-based lead discovery has emerged as one of the most efficient screening strategies for finding hit molecules in drug discovery. Recently, a novel strategy based on a class of fragments characterized by an ultralow molecular weight (ULMW) has been proposed. These fragments bind to the target with a very low affinity, requiring reliable biophysical methods for detection. The most notable application of ULMW used a set of 81 fragments, named MiniFrags, and screened them by X-ray...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Fragment-Based Nuclear Magnetic Resonance Screen against a Regulator of G Protein Signaling Identifies a Binding ... - Wiley Fragment-Based Nuclear Magnetic Resonance Screen against a Regulator of G Protein Signaling Identifies a Binding ... Wiley Fragment-Based Nuclear Magnetic Resonance Screen against a Regulator of G Protein Signaling Identifies a Binding ... - Wiley More...	nmrlearner	Online News	0	04-14-2023 10:26 PM
Medium-Throughput Screen of Microbially Produced Serotoninvia a G-Protein-Coupled Receptor-Based Sensor Medium-Throughput Screen of Microbially Produced Serotoninvia a G-Protein-Coupled Receptor-Based Sensor http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.7b00605/20170825/images/medium/bi-2017-006057_0005.gif Biochemistry DOI: 10.1021/acs.biochem.7b00605 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/cNPBRunl2u8 More...	nmrlearner	Journal club	0	08-29-2017 01:33 AM
[NMR paper] Application of comprehensive NMR-based analysis strategy in annotation, isolation and structure elucidation of low molecular weight metabolites of Ricinus communis seeds. Application of comprehensive NMR-based analysis strategy in annotation, isolation and structure elucidation of low molecular weight metabolites of Ricinus communis seeds. Related Articles Application of comprehensive NMR-based analysis strategy in annotation, isolation and structure elucidation of low molecular weight metabolites of Ricinus communis seeds. Phytochem Anal. 2015 Oct 14; Authors: Vu?kovi? I, Rapinoja ML, Vaismaa M, Vanninen P, Koskela H Abstract INTRODUCTION: Powder-like extract of Ricinus communis seeds contain a...	nmrlearner	Journal club	0	10-16-2015 01:44 PM
[NMR paper] A Cost-Effective Protocol for the Parallel Production of Libraries of (13)CH 3-Specifically Labeled Mutants for NMR Studies of High Molecular Weight Proteins. A Cost-Effective Protocol for the Parallel Production of Libraries of (13)CH 3-Specifically Labeled Mutants for NMR Studies of High Molecular Weight Proteins. Related Articles A Cost-Effective Protocol for the Parallel Production of Libraries of (13)CH 3-Specifically Labeled Mutants for NMR Studies of High Molecular Weight Proteins. Methods Mol Biol. 2014;1091:229-44 Authors: Crublet E, Kerfah R, Mas G, Noirclerc-Savoye M, Lantez V, Vernet T, Boisbouvier J Abstract There is increasing interest in applying NMR spectroscopy to the study of...	nmrlearner	Journal club	0	11-11-2013 01:30 AM
Cracking the molecular weight barrier: Fragment screening of an aminotransferase using an NMR-based functional assay. Cracking the molecular weight barrier: Fragment screening of an aminotransferase using an NMR-based functional assay. Cracking the molecular weight barrier: Fragment screening of an aminotransferase using an NMR-based functional assay. Bioorg Med Chem Lett. 2011 Jul 21; Authors: Mendoza R, Petros AM, Liu Y, Thimmapaya R, Surowy CS, Leise WF, Pereda-Lopez A, Panchal SC, Sun C NMR-based screening of protein targets has become a well established part of the drug discovery process especially with respect to fragments. However, as target size increases...	nmrlearner	Journal club	0	08-16-2011 01:19 PM
Alanine Methyl Groups as NMR Probes of Molecular Structure and Dynamics in High-Molecular-Weight Proteins Alanine Methyl Groups as NMR Probes of Molecular Structure and Dynamics in High-Molecular-Weight Proteins Raquel Godoy-Ruiz, Chenyun Guo and Vitali Tugarinov http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja1083656/aop/images/medium/ja-2010-083656_0009.gif Journal of the American Chemical Society DOI: 10.1021/ja1083656 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/hxZ4cabF688	nmrlearner	Journal club	0	12-08-2010 10:04 AM
[NMR paper] Design and characterization of libraries of molecular fragments for use in NMR screen Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets. Related Articles Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets. J Chem Inf Comput Sci. 2004 Nov-Dec;44(6):2157-66 Authors: Baurin N, Aboul-Ela F, Barril X, Davis B, Drysdale M, Dymock B, Finch H, Fromont C, Richardson C, Simmonite H, Hubbard RE We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein...	nmrlearner	Journal club	0	11-24-2010 10:03 PM
[NMR paper] NMR-based binding screen and structural analysis of the complex formed between alpha- NMR-based binding screen and structural analysis of the complex formed between alpha-cobratoxin and an 18-mer cognate peptide derived from the alpha 1 subunit of the nicotinic acetylcholine receptor from Torpedo californica. Related Articles NMR-based binding screen and structural analysis of the complex formed between alpha-cobratoxin and an 18-mer cognate peptide derived from the alpha 1 subunit of the nicotinic acetylcholine receptor from Torpedo californica. J Biol Chem. 2002 Oct 4;277(40):37439-45 Authors: Zeng H, Hawrot E The alpha18-mer...	nmrlearner	Journal club	0	11-24-2010 08:58 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