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 11-19-2010, 08:29 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,137
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 HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structu

HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.

Related Articles HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.

J Magn Reson. 2000 Nov;147(1):138-46

Authors: García de la Torre J, Huertas ML, Carrasco B

The heteronuclear NMR relaxation of globular proteins depends on the anisotropic rotational diffusion tensor. Using our previous developments for prediction of hydrodynamic properties of arbitrarily shaped particles, by means of bead models, we have constructed a computational procedure to calculate the rotational diffusion tensor and other properties of proteins from their detailed, atomic-level structure. From the atomic coordinates file used to build the bead model, the orientation of the pertinent dipoles can be extracted and combined with the hydrodynamic information to predict, for each residue in the protein, the relaxation times. All of these developments have been implemented in a computer program, HYDRONMR, which will be of public domain.

PMID: 11042057 [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
iHADAMAC: a complementary tool for sequential resonance assignment of globular and highly disordered proteins
iHADAMAC: a complementary tool for sequential resonance assignment of globular and highly disordered proteins Publication year: 2011 Source: Journal of Magnetic Resonance, Available online 9 November 2011</br> Sophie*Feuerstein, Michael J.*Plevin, Dieter*Willbold, Bernhard*Brutscher</br> An experiment, iHADAMAC, is presented that yields information on the amino-acid type of individual residues in a protein by editing theH-N correlations into 7 different 2D spectra, each corresponding to a different class of amino-acid types. Amino-acid type discrimination is realized via a Hadamard...
nmrlearner Journal club 0 11-10-2011 07:38 AM
Nonnative Interactions in the FF Domain Folding Pathway from an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study
Nonnative Interactions in the FF Domain Folding Pathway from an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study Dmitry M. Korzhnev, Robert M. Vernon, Tomasz L. Religa, Alexandar L. Hansen, David Baker, Alan R. Fersht and Lewis E. Kay http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja203686t/aop/images/medium/ja-2011-03686t_0002.gif Journal of the American Chemical Society DOI: 10.1021/ja203686t http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
nmrlearner Journal club 0 06-29-2011 04:45 AM
Non-Native Interactions in the FF Domain Folding Pathway From an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study.
Non-Native Interactions in the FF Domain Folding Pathway From an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study. Non-Native Interactions in the FF Domain Folding Pathway From an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study. J Am Chem Soc. 2011 Jun 6; Authors: Korzhnev DM, Vernon RM, Religa TL, Hansen AL, Baker D, Fersht AR, Kay LE Several all-helical single-domain proteins have been shown to fold rapidly (us timescale) to a compact...
nmrlearner Journal club 0 06-07-2011 11:05 AM
[NMR tweet] @Michael_Haz It's like we're in the midst of a gigantic magnetic resonance absorption. Radiation makes nuclear spins flip at atomic level.
@Michael_Haz It&apos;s like we&apos;re in the midst of a gigantic magnetic resonance absorption. Radiation makes nuclear spins flip at atomic level. Published by chickelit (Bruce B.) on 2011-02-09T19:11:44Z Source: Twitter
nmrlearner Twitter NMR 0 02-09-2011 07:34 PM
[NMR paper] Contact model for the prediction of NMR N-H order parameters in globular proteins.
Contact model for the prediction of NMR N-H order parameters in globular proteins. Related Articles Contact model for the prediction of NMR N-H order parameters in globular proteins. J Am Chem Soc. 2002 Oct 30;124(43):12654-5 Authors: Zhang F, Brüschweiler R An analytical relationship is presented for the estimation of NMR S2 order parameters of N-HN vectors of the protein backbone from high-resolution protein structures. The relationship solely depends on close contacts of the peptide plane to the rest of the protein. Application of the...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic cal
Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR. Related Articles Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR. J Biomol NMR. 2002 Jun;23(2):139-50 Authors: Bernadó P, García de la Torre J, Pons M HYDRONMR is an implementation of state of the art hydrodynamic modeling to calculate the spectral density functions for NH or C(alpha)-H vectors in a rigid protein structure starting from an atomic level representation. Thus...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] The structure and dipole moment of globular proteins in solution and crystalline stat
The structure and dipole moment of globular proteins in solution and crystalline states: use of NMR and X-ray databases for the numerical calculation of dipole moment. Related Articles The structure and dipole moment of globular proteins in solution and crystalline states: use of NMR and X-ray databases for the numerical calculation of dipole moment. Biopolymers. 2001 Apr 5;58(4):398-409 Authors: Takashima S The large dipole moment of globular proteins has been well known because of the detailed studies using dielectric relaxation and...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] High-level 2H/13C/15N labeling of proteins for NMR studies.
High-level 2H/13C/15N labeling of proteins for NMR studies. Related Articles High-level 2H/13C/15N labeling of proteins for NMR studies. J Biomol NMR. 1995 Jun;5(4):339-44 Authors: Venters RA, Huang CC, Farmer BT, Trolard R, Spicer LD, Fierke CA The protein human carbonic anhydrase II (HCA II) has been isotopically labeled with 2H, 13C and 15N for high-resolution NMR assignment studies and pulse sequence development. To increase the sensitivity of several key 1H/13C/15N triple-resonance correlation experiments, 2H has been incorporated into...
nmrlearner Journal club 0 08-22-2010 03:41 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 07:54 AM.


Map