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 03-05-2016, 11:21 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,617
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-based determination of the 3D structure of the ligand-protein interaction site without protein resonance assignment.

NMR-based determination of the 3D structure of the ligand-protein interaction site without protein resonance assignment.

NMR-based determination of the 3D structure of the ligand-protein interaction site without protein resonance assignment.

J Am Chem Soc. 2016 Mar 4;

Authors: Orts J, Wälti MA, Marsh M, Vera L, Gossert AD, Güntert P, Riek R

Abstract
Molecular replacement in X-ray crystallography is the prime method for establishing structure-activity relationships of pharmaceutically relevant molecules. Such an approach is not available for NMR. Here, we establish a comparable method, called NMR molecular replacement (NMR2). The method requires experimentally measured ligand intra-molecular NOEs and ligand-protein inter-molecular NOEs as well as a previously known receptor structure or model. Our findings demonstrate that NMR2 may open a new avenue for the fast and robust determination of the interaction site of ligand-protein complex- es at atomic resolution.


PMID: 26943491 [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
Parameterization of Solvent-Protein Interaction and Its Use on NMR Protein Structure Determination
Parameterization of Solvent-Protein Interaction and Its Use on NMR Protein Structure Determination Publication year: 2012 Source:Journal of Magnetic Resonance</br> Yu Wang, Charles D. Schwieters, Nico Tjandra</br> NMR structure determination is frequently hindered by an insufficient amount of distance information for determining the correct fold of the protein in its early stages. In response we introduce a simple and general structure-based metric that can be used to incorporate NMR-based restraints on protein surface accessibility. This metric is inversely...
nmrlearner Journal club 0 06-07-2012 06:58 AM
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach. Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach. Methods Enzymol. 2011;493:241-75 Authors: Ziarek JJ, Peterson FC, Lytle BL, Volkman BF Over the last 15years, the role of NMR spectroscopy in the lead identification and optimization stages of pharmaceutical drug discovery has steadily increased. NMR occupies a unique niche in the biophysical analysis of drug-like...
nmrlearner Journal club 0 03-05-2011 01:02 PM
Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies.
Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies. Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies. J Am Chem Soc. 2010 Dec 16; Authors: Gossert AD, Hiller S, Ferna?ndez C The detection and structural characterization of protein-ligand interactions by solution NMR is central to functional biology research as well as to drug discovery. Here we present a robust and highly automated procedure for obtaining the resonance assignments necessary for studies of such...
nmrlearner Journal club 0 12-18-2010 12:00 PM
A novel strategy for NMR resonance assignment and protein structure determination
A novel strategy for NMR resonance assignment and protein structure determination Abstract The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution â?? especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a...
nmrlearner Journal club 0 12-18-2010 01:31 AM
A novel strategy for NMR resonance assignment and protein structure determination.
A novel strategy for NMR resonance assignment and protein structure determination. A novel strategy for NMR resonance assignment and protein structure determination. J Biomol NMR. 2010 Dec 14; Authors: Lemak A, Gutmanas A, Chitayat S, Karra M, Farès C, Sunnerhagen M, Arrowsmith CH The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed...
nmrlearner Journal club 0 12-17-2010 11:23 AM
Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies
Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies Alvar D. Gossert, Sebastian Hiller and Ce?sar Ferna?ndez http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja108383x/aop/images/medium/ja-2010-08383x_0004.gif Journal of the American Chemical Society DOI: 10.1021/ja108383x http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/E3PMYeBSCeE
nmrlearner Journal club 0 12-17-2010 12:50 AM
Robust structure-based resonance assignment for functional protein studies by NMR
Abstract High-throughput functional protein NMR studies, like protein interactions or dynamics, require an automated approach for the assignment of the protein backbone. With the availability of a growing number of protein 3D structures, a new class of automated approaches, called structure-based assignment, has been developed quite recently. Structure-based approaches use primarily NMR input data that are not based on J-coupling and for which connections between residues are not limited by through bonds magnetization transfer efficiency. We present here a robust structure-based assignment...
nmrlearner Journal club 0 08-14-2010 04:19 AM


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 - 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 08:38 AM.


Map