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 08-21-2010, 11:53 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 "Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applie

"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin.

Related Articles "Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin.

Proteins. 1993 Apr;15(4):385-400

Authors: Bonvin AM, Rullmann JA, Lamerichs RM, Boelens R, Kaptein R

The structure in solution of crambin, a small protein of 46 residues, has been determined from 2D NMR data using an iterative relaxation matrix approach (IRMA) together with distance geometry, distance bound driven dynamics, molecular dynamics, and energy minimization. A new protocol based on an "ensemble" approach is proposed and compared to the more standard initial rate analysis approach and a "single structure" relaxation matrix approach. The effects of fast local motions are included and R-factor calculations are performed on NOE build-ups to describe the quality of agreement between theory and experiment. A new method for stereospecific assignment of prochiral groups, based on a comparison of theoretical and experimental NOE intensities, has been applied. The solution structure of crambin could be determined with a precision (rmsd from the average structure) of 0.7 A on backbone atoms and 1.1 A on all heavy atoms and is largely similar to the crystal structure with a small difference observed in the position of the side chain of Tyr-29 which is determined in solution by both J-coupling and NOE data. Regions of higher structural variability (suggesting higher mobility) are found in the solution structure, in particular for the loop between the two helices (Gly-20 to Pro-22).

PMID: 8460109 [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
[NMR tweet] CERN NASA "optical nuclear magnetic resonance" google.com.
CERN NASA "optical nuclear magnetic resonance" google.com. Published by jfdslkjfdslkfj (jfdslkjf dslkfj) on 2011-05-06T14:37:11Z Source: Twitter
nmrlearner Twitter NMR 0 05-06-2011 02:44 PM
[NMR tweet] How is "Tyrannosaurus" related to "Nuclear Magnetic Resonance"? http://www.threewiki.com/60YeHE @threewiki
How is "Tyrannosaurus" related to "Nuclear Magnetic Resonance"? http://www.threewiki.com/60YeHE @threewiki Published by Jakob7 (Jakob Baumhardt) on 2010-12-04T05:24:13Z Source: Twitter
nmrlearner Twitter NMR 0 12-04-2010 05:30 AM
[Question from NMRWiki Q&A forum] What is the easiest way to emulate the "array" command from VNMR in XWINNMR/TOPSPIN?
What is the easiest way to emulate the "array" command from VNMR in XWINNMR/TOPSPIN? What is the easiest way to emulate the "array" command from VNMR in XWINNMR/TOPSPIN? I recently moved from a lab using a Varian (Unity plus 500) with VNMR 6.whatever to a lab with only Bruker (AVANCE 300/400/500) spectrometers available. I am used to using the "array" caommand in VNMR and viewing the spectra with "dssa" or "dssh." I don't know a convenient way to do the same thing in XWINNMR. I know there are some AU programs but I'm not sure what they all do or if what I want is available. I tried...
nmrlearner News from other NMR forums 0 09-24-2010 07:36 PM
[NMR paper] Complete relaxation matrix refinement of NMR structures of proteins using analyticall
Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities. Related Articles Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities. J Biomol NMR. 1991 Sep;1(3):257-69 Authors: Mertz JE, Güntert P, Wüthrich K, Braun W A new method for refining three-dimensional (3D) NMR structures of proteins is described, which takes account of the complete relaxation pathways....
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] Complete relaxation matrix refinement of NMR structures of proteins using analyticall
Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities. Related Articles Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities. J Biomol NMR. 1991 Sep;1(3):257-69 Authors: Mertz JE, Güntert P, Wüthrich K, Braun W A new method for refining three-dimensional (3D) NMR structures of proteins is described, which takes account of the complete relaxation pathways....
nmrlearner Journal club 0 08-21-2010 11:12 PM
Postdoctoral Position "Solution Dynamics of Protein Kinases" in New York
Postdoctoral Position "Solution Dynamics of Protein Kinases" in New York A postdoctoral position to study the solution dynamics and structure of protein kinases is available on a NIH funded project (REF#: HS-R-6453-10-08-S). Our group is interested in how static and dynamic changes of protein structure affect the activity of protein kinases. We combine X-ray crystallography, NMR and ligand binding kinetics with collaborative molecular dynamic studies (See e.g. ref 1 and 2). Our research group is located at Stony Brook University in a highly interactive environment with the New York...
nmrlearner Job marketplace 0 08-21-2010 05:17 AM
Postdoctoral Position "Solution Dynamics of Protein Kinases" in New York
Postdoctoral Position "Solution Dynamics of Protein Kinases" in New York A postdoctoral position to study the solution dynamics and structure of protein kinases is available on a NIH funded project (REF#: HS-R-6453-10-08-S). Our group is interested in how static and dynamic changes of protein structure affect the activity of protein kinases. We combine X-ray crystallography, NMR and ligand binding kinetics with collaborative molecular dynamic studies (See e.g. ref 1 and 2). Our research group is located at Stony Brook University in a highly interactive environment with the New York...
nmrlearner Job marketplace 0 08-21-2010 05:14 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 11:33 AM.


Map