BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search
Home Forums Wiki NMR feeds Downloads Register Today's Posts



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 10-11-2017, 10:37 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,187
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default NMR studies of ligand binding.

NMR studies of ligand binding.

NMR studies of ligand binding.

Curr Opin Struct Biol. 2017 Oct 07;48:16-22

Authors: Nitsche C, Otting G

Abstract
NMR spectroscopy is an established tool in drug discovery, but its strength is commonly regarded to be largely confined to the early stages of hit discovery and fragment based drug design, where NMR offers unique capabilities of characterizing the binding modes of ligand molecules that bind sufficiently weakly to be in rapid exchange between bound and free state. Here we, first, provide a meta-review of recent reviews on NMR studies of ligand binding and, second, review recent progress towards NMR characterization of the ligand binding mode in stable protein-ligand complexes, with particular emphasis on the global positioning system (GPS) approach enabled by paramagnetic lanthanide tags.


PMID: 29017071 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Periplasmic Binding Protein Dimer Has a Second AllostericEvent Tied to Ligand Binding
Periplasmic Binding Protein Dimer Has a Second AllostericEvent Tied to Ligand Binding http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.7b00657/20170922/images/medium/bi-2017-00657x_0006.gif Biochemistry DOI: 10.1021/acs.biochem.7b00657 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/kcJzvDujZt8 More...
nmrlearner Journal club 0 09-23-2017 05:52 AM
Determination of ligand binding modes in weak proteinā??ligand complexes using sparse NMR data
Determination of ligand binding modes in weak proteinā??ligand complexes using sparse NMR data Abstract We describe a general approach to determine the binding pose of small molecules in weakly bound proteinā??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
[NMR paper] Over-expression and purification of isotopically labeled recombinant ligand-binding domain of orphan nuclear receptor human B1-binding factor/human liver receptor homologue 1 for NMR studies.
Over-expression and purification of isotopically labeled recombinant ligand-binding domain of orphan nuclear receptor human B1-binding factor/human liver receptor homologue 1 for NMR studies. Related Articles Over-expression and purification of isotopically labeled recombinant ligand-binding domain of orphan nuclear receptor human B1-binding factor/human liver receptor homologue 1 for NMR studies. Protein Expr Purif. 2006 Jan;45(1):99-106 Authors: Chen X, Tong X, Xie Y, Wang Y, Ma J, Gao D, Wu H, Chen H The human hepatitis B virus enhancer II...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] Low 13C-background for NMR-based studies of ligand binding using 13C-depleted glucose
Low 13C-background for NMR-based studies of ligand binding using 13C-depleted glucose as carbon source for microbial growth: 13C-labeled glucose and 13C-forskolin binding to the galactose-H+ symport protein GalP in Escherichia coli. Related Articles Low 13C-background for NMR-based studies of ligand binding using 13C-depleted glucose as carbon source for microbial growth: 13C-labeled glucose and 13C-forskolin binding to the galactose-H+ symport protein GalP in Escherichia coli. J Am Chem Soc. 2004 Jan 14;126(1):86-7 Authors: Patching SG, Herbert RB,...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] NMR analysis of site-specific ligand binding in oligomeric proteins. Dynamic studies
NMR analysis of site-specific ligand binding in oligomeric proteins. Dynamic studies on the interaction of riboflavin synthase with trifluoromethyl-substituted intermediates. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles NMR analysis of site-specific ligand binding in oligomeric proteins. Dynamic studies on the interaction of riboflavin synthase with trifluoromethyl-substituted intermediates. Biochemistry. 1996 Jul 30;35(30):9637-46 Authors: Scheuring J, Fischer M, Cushman M, Lee J, Bacher A,...
nmrlearner Journal club 0 08-22-2010 02:20 PM
[NMR paper] 15N NMR relaxation studies of the FK506 binding protein: dynamic effects of ligand bi
15N NMR relaxation studies of the FK506 binding protein: dynamic effects of ligand binding and implications for calcineurin recognition. Related Articles 15N NMR relaxation studies of the FK506 binding protein: dynamic effects of ligand binding and implications for calcineurin recognition. Biochemistry. 1994 Apr 12;33(14):4093-100 Authors: Cheng JW, Lepre CA, Moore JM Backbone dynamics of the ligand- (FK506-) bound protein FKBP-12 (107 amino acids) have been examined using 15N relaxation data derived from inverse-detected two-dimensional...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] 15N NMR relaxation studies of the FK506 binding protein: dynamic effects of ligand bi
15N NMR relaxation studies of the FK506 binding protein: dynamic effects of ligand binding and implications for calcineurin recognition. Related Articles 15N NMR relaxation studies of the FK506 binding protein: dynamic effects of ligand binding and implications for calcineurin recognition. Biochemistry. 1994 Apr 12;33(14):4093-100 Authors: Cheng JW, Lepre CA, Moore JM Backbone dynamics of the ligand- (FK506-) bound protein FKBP-12 (107 amino acids) have been examined using 15N relaxation data derived from inverse-detected two-dimensional...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] An investigation of the ligand-binding site of the glutamine-binding protein of Esche
An investigation of the ligand-binding site of the glutamine-binding protein of Escherichia coli using rotational-echo double-resonance NMR. Related Articles An investigation of the ligand-binding site of the glutamine-binding protein of Escherichia coli using rotational-echo double-resonance NMR. Biochemistry. 1994 Jul 26;33(29):8651-61 Authors: Hing AW, Tjandra N, Cottam PF, Schaefer J, Ho C Glutamine-binding protein (GlnBP) is an essential component of the glutamine transport system in Escherichia coli. Rotational-echo double-resonance...
nmrlearner Journal club 0 08-22-2010 03:29 AM



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



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 04:49 PM.


Map