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



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 07-16-2014, 10:46 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 19,995
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 Comparing Binding Modes of Analogous Fragments Using NMR in Fragment-Based Drug Design: Application to PRDX5.

Comparing Binding Modes of Analogous Fragments Using NMR in Fragment-Based Drug Design: Application to PRDX5.

Comparing Binding Modes of Analogous Fragments Using NMR in Fragment-Based Drug Design: Application to PRDX5.

PLoS One. 2014;9(7):e102300

Authors: Aguirre C, Brink TT, Guichou JF, Cala O, Krimm I

Abstract
Fragment-based drug design is one of the most promising approaches for discovering novel and potent inhibitors against therapeutic targets. The first step of the process consists of identifying fragments that bind the protein target. The determination of the fragment binding mode plays a major role in the selection of the fragment hits that will be processed into drug-like compounds. Comparing the binding modes of analogous fragments is a critical task, not only to identify specific interactions between the protein target and the fragment, but also to verify whether the binding mode is conserved or differs according to the fragment modification. While X-ray crystallography is the technique of choice, NMR methods are helpful when this fails. We show here how the ligand-observed saturation transfer difference (STD) experiment and the protein-observed 15N-HSQC experiment, two popular NMR screening experiments, can be used to compare the binding modes of analogous fragments. We discuss the application and limitations of these approaches based on STD-epitope mapping, chemical shift perturbation (CSP) calculation and comparative CSP sign analysis, using the human peroxiredoxin 5 as a protein model.


PMID: 25025339 [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
[NMR paper] Structure-based drug design: NMR-based approach for ligand-protein interactions.
Structure-based drug design: NMR-based approach for ligand-protein interactions. Related Articles Structure-based drug design: NMR-based approach for ligand-protein interactions. Drug Discov Today Technol. 2006;3(3):241-5 Authors: Zhang X, Tang H, Ye C, Liu M Abstract The realization of the powerfulness in analyzing ligand-protein interactions at the atomic resolution has made NMR techniques increasingly attractive in drug discovery and development. With some significant new method developments during the past few years,...
nmrlearner Journal club 0 07-06-2014 08:28 PM
[NMR paper] Solution NMR analyses of the C-type carbohydrate recognition domain of DC-SIGNR reveal different binding modes for HIV-derived oligosaccharides and smaller glycan fragments.
Solution NMR analyses of the C-type carbohydrate recognition domain of DC-SIGNR reveal different binding modes for HIV-derived oligosaccharides and smaller glycan fragments. Related Articles Solution NMR analyses of the C-type carbohydrate recognition domain of DC-SIGNR reveal different binding modes for HIV-derived oligosaccharides and smaller glycan fragments. J Biol Chem. 2013 Jun 20; Authors: Probert F, Whittaker SB, Crispin M, Mitchell DA, Dixon AM Abstract The C-type lectin DC-SIGNR (Dendritic Cell-Specific ICAM-3-Grabbing...
nmrlearner Journal club 0 06-25-2013 12:17 AM
Structure-Based Drug Design
Structure-Based Drug Design http://www.spectroscopynow.com/common/images/thumbnails/no_img.gifThe 13th Structure-Based Drug Discovery conference will feature the development of in silico technology as well as experimental approaches useful for accurately predicting and modeling the structures of proteins in structure-based drug design efforts. More...
nmrlearner Conferences 0 05-22-2013 04:43 PM
[NMR paper] Computer-Aided Design of Fragment Mixtures for NMR-Based Screening.
Computer-Aided Design of Fragment Mixtures for NMR-Based Screening. Related Articles Computer-Aided Design of Fragment Mixtures for NMR-Based Screening. PLoS One. 2013;8(3):e58571 Authors: Arroyo X, Goldflam M, Feliz M, Belda I, Giralt E Abstract Fragment-based drug discovery is widely applied both in industrial and in academic screening programs. Several screening techniques rely on NMR to detect binding of a fragment to a target. NMR-based methods are among the most sensitive techniques and have the further advantage of yielding a low...
nmrlearner Journal club 0 03-22-2013 06:10 PM
NMR and protein structure in drug design: application to cyclotides and conotoxins.
NMR and protein structure in drug design: application to cyclotides and conotoxins. NMR and protein structure in drug design: application to cyclotides and conotoxins. Eur Biophys J. 2011 Feb 3; Authors: Daly NL, Rosengren KJ, Troeira Henriques S, Craik DJ Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique for determining the structures, dynamics and interactions of molecules, and the derived information can be useful in drug design applications. This article gives a brief overview of the role of NMR in drug design and...
nmrlearner Journal club 0 02-04-2011 11:34 AM
[BMNRC community] NMR-based screening: a powerful tool in fragment-based drug discovery
NMR-based screening: a powerful tool in fragment-based drug discovery http://www.rsc.org/delivery/_ArticleLinking/DisplayHTMLArticleforfree.cfm?JournalCode=AN&Year=2007&ManuscriptID=b709658p&Iss=7 Go to BMNRC community to find more info about this topic.
nmrlearner News from other NMR forums 0 09-02-2010 04:59 AM
[NMR paper] NMR spectroscopy in structure-based drug design.
NMR spectroscopy in structure-based drug design. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles NMR spectroscopy in structure-based drug design. Curr Opin Biotechnol. 1999 Feb;10(1):42-7 Authors: Roberts GC NMR methods for the study of motion in proteins continue to improve, and a number of studies of protein-ligand complexes relevant to drug design have been reported over the past year, for example, studies of fatty-acid-binding protein and SH2 and SH3 domains. These...
nmrlearner Journal club 0 08-21-2010 04:03 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



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



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2020, 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 02:14 AM.


Map