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 11-24-2010, 08:49 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,751
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 Structures of protein-protein complexes are docked using only NMR restraints from res

Structures of protein-protein complexes are docked using only NMR restraints from residual dipolar coupling and chemical shift perturbations.

Related Articles Structures of protein-protein complexes are docked using only NMR restraints from residual dipolar coupling and chemical shift perturbations.

J Am Chem Soc. 2002 Mar 13;124(10):2104-5

Authors: McCoy MA, Wyss DF

NMR structures of protein-protein and protein-ligand complexes rely heavily on intermolecular NOEs. Recent work has shown that if no significant conformational changes occur upon complex formation residual dipolar coupling can replace most of the NOE restraints in protein-protein complexes, while restraints derived from chemical shift perturbations can largely replace intermolecular NOEs in protein-ligand structures. By combining restraints from chemical shift perturbations with orientation restraints derived from measurements of residual dipolar couplings, we show that the structure of the EIN-HPr complex can be calculated without NOE restraints. The final structure, built from the crystal structures of EIN and HPr in their uncomplexed form and docked only with NMR restraints, places HPr within 2.5 A of the position determined from the mean NMR structure of the complex.

PMID: 11878950 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints.
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints. Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints. J Am Chem Soc. 2011 Apr 4; Authors: Ryabov Y, Schwieters CD, Clore GM (15)N R(2)/R(1) relaxation data contain information on molecular shape and size as well as on bond vector orientations relative to...
nmrlearner Journal club 0 04-06-2011 10:54 AM
Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints
Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints Yaroslav Ryabov, Charles D. Schwieters and G. Marius Clore http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja201020c/aop/images/medium/ja-2011-01020c_0002.gif Journal of the American Chemical Society DOI: 10.1021/ja201020c http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/3J1IyCLkQMQ
nmrlearner Journal club 0 04-05-2011 10:37 AM
[NMR paper] GENFOLD: a genetic algorithm for folding protein structures using NMR restraints.
GENFOLD: a genetic algorithm for folding protein structures using NMR restraints. Related Articles GENFOLD: a genetic algorithm for folding protein structures using NMR restraints. Protein Sci. 1998 Feb;7(2):491-9 Authors: Bayley MJ, Jones G, Willett P, Williamson MP We report the development and validation of the program GENFOLD, a genetic algorithm that calculates protein structures using restraints obtained from NMR, such as distances derived from nuclear Overhauser effects, and dihedral angles derived from coupling constants. The program...
nmrlearner Journal club 0 11-17-2010 11:06 PM
[NMR paper] Determining the structures of large proteins and protein complexes by NMR.
Determining the structures of large proteins and protein complexes by NMR. Related Articles Determining the structures of large proteins and protein complexes by NMR. Trends Biotechnol. 1998 Jan;16(1):22-34 Authors: Clore GM, Gronenborn AM Recent advances in multidimensional NMR methodology to obtain 1H, 15N and 13C resonance assignments, interproton-distance and torsion-angle restraints, and restraints that characterize long-range order have, coupled with new methods of structure refinement, permitted solution structure of proteins in excess...
nmrlearner Journal club 0 11-17-2010 11:06 PM
[NMR paper] NMR structures of proteins and protein complexes beyond 20,000 M(r).
NMR structures of proteins and protein complexes beyond 20,000 M(r). Related Articles NMR structures of proteins and protein complexes beyond 20,000 M(r). Nat Struct Biol. 1997 Oct;4 Suppl:849-53 Authors: Clore GM, Gronenborn AM Recent advances in multidimensional NMR to obtain resonance assignments, interproton distance and torsion angle restraints, and restraints that characterize long range order, coupled with new methods of structure refinement, have permitted solution structures of proteins in excess of 250 residues to be solved.
nmrlearner Journal club 0 08-22-2010 05:08 PM
[NMR paper] Structures of larger proteins, protein-ligand and protein-DNA complexes by multi-dime
Structures of larger proteins, protein-ligand and protein-DNA complexes by multi-dimensional heteronuclear NMR. Related Articles Structures of larger proteins, protein-ligand and protein-DNA complexes by multi-dimensional heteronuclear NMR. Prog Biophys Mol Biol. 1994;62(2):153-84 Authors: Clore GM, Gronenborn AM
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] Structures of larger proteins, protein-ligand and protein-DNA complexes by multi-dime
Structures of larger proteins, protein-ligand and protein-DNA complexes by multi-dimensional heteronuclear NMR. Related Articles Structures of larger proteins, protein-ligand and protein-DNA complexes by multi-dimensional heteronuclear NMR. Prog Biophys Mol Biol. 1994;62(2):153-84 Authors: Clore GM, Gronenborn AM
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] NMR studies of protein-nucleic acid complexes: structures, solvation, dynamics and co
NMR studies of protein-nucleic acid complexes: structures, solvation, dynamics and coupled protein folding. Related Articles NMR studies of protein-nucleic acid complexes: structures, solvation, dynamics and coupled protein folding. Q Rev Biophys. 1999 Feb;32(1):57-98 Authors: Härd T
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 - 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 11:35 AM.


Map