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 04-29-2006, 10:39 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
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



Combining NMR Relaxation with Chemical Shift Perturbation Data to Drive Protein-protein Docking.
J Biomol NMR. 2006 Apr;34(4):237-44.

van Dijk AD, Kaptein R, Boelens R, Bonvin AM.

NMR Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, 3584CH, Utrecht, The Netherlands, a.m.j.j.bonvin@chem.uu.nl.

The modeling of biomolecular complexes by computational docking using the known structures of their constituents is developing rapidly to become a powerful tool in structural biology. It is especially useful in combination with even limited experimental information describing the interface. Here we demonstrate for the first time the use of diffusion anisotropy in combination with chemical shift perturbation data to drive protein-protein docking. For validation purposes we make use of simulated diffusion anisotropy data. Inclusion of this information, which can be derived from NMR relaxation rates and reports on the orientation of the components of a complex with respect to the rotational diffusion tensor, substantially improves the docking results
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR images] Chemical Shifts in NMR Spectra
http://hyperphysics.phy-astr.gsu.edu/hbase/nuclear/imgnuc/cshift.gif hyperphysics.phy-astr.gsu.edu 5/07/2011 6:04:05 PM GMT Chemical Shifts in NMR Spectra More...
nmrlearner NMR pictures 0 07-26-2011 11:22 PM
19F chemical shifts.jpg
http://upload.wikimedia.org/wikimedia/commons/thumb/2/2e/19F_chemical_shifts.jpg/300px-19F_chemical_shifts.jpg Uploaded by user "Artb33" on Sun, 06 Mar 2011 14:16:00 UTC Added to category on Sun, 06 Mar 2011 14:16:18 UTC Original image: 11812×8197 pixel; 1.905.499 bytes. Licensing : CC-BY-SA,GFDL 19F chemical shifts.jpg More...
nmrlearner NMR pictures 0 03-06-2011 03:35 PM
19F chemical shifts.tif
http://upload.wikimedia.org/wikimedia/commons/thumb/2/22/19F_chemical_shifts.tif/300px-19F_chemical_shifts.tif Uploaded by user "Artb33" on Sun, 06 Mar 2011 14:07:00 UTC Added to category on Sun, 06 Mar 2011 14:07:36 UTC Original image: 11812×8197 pixel; 79.932 bytes. Licensing : CC-BY-SA,GFDL 19F chemical shifts.tif More...
nmrlearner NMR pictures 0 03-06-2011 03:35 PM
[NMR paper] Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data.
Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Related Articles Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Proteins. 2005 Aug 15;60(3):367-81 Authors: van Dijk AD, Fushman D, Bonvin AM When classical, Nuclear Overhauser Effect (NOE)-based approaches fail, it is possible, given high-resolution...
nmrlearner Journal club 0 12-01-2010 06:56 PM
Measurement of carbonyl chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy: comparison between uniformly and selectively 13C labeled samples
Measurement of carbonyl chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy: comparison between uniformly and selectively 13C labeled samples Patrik Lundström, D. Flemming Hansen and Lewis E. Kay Journal of Biomolecular NMR; 2008; 42(1); pp 35 - 47 Abstract: Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion nuclear magnetic resonance (NMR) spectroscopy has emerged as a powerful method for quantifying chemical shifts of excited protein states. For many applications of the technique that involve the measurement of relaxation rates of carbon...
Abe Journal club 0 09-21-2008 11:36 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 - 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 09:32 PM.


Map