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 01-28-2015, 05:28 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 Motion and Conformational Entropy in Protein Function: Creation of an NMR-Based Entropy Meter

Motion and Conformational Entropy in Protein Function: Creation of an NMR-Based Entropy Meter

Publication date: 27 January 2015
Source:Biophysical Journal, Volume 108, Issue 2, Supplement 1

Author(s): Vignesh Kasinath , Kyle W. Harpole , Veronica R. Moorman , Kathleen G. Valentine , Kendra K. Frederick , Kim A. Sharp , Joshua Wand









More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations.
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations. Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations. Proc Natl Acad Sci U S A. 2014 Oct 13; Authors: Baxa MC, Haddadian EJ, Jumper JM, Freed KF, Sosnick TR Abstract The loss of conformational entropy is a major contribution in the thermodynamics of protein folding. However, accurate determination of the quantity...
nmrlearner Journal club 0 10-15-2014 10:58 AM
MicroscopicInsights into the NMR Relaxation-BasedProtein Conformational Entropy Meter
MicroscopicInsights into the NMR Relaxation-BasedProtein Conformational Entropy Meter Vignesh Kasinath, Kim A. Sharp and A. Joshua Wand http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja405200u/aop/images/medium/ja-2013-05200u_0006.gif Journal of the American Chemical Society DOI: 10.1021/ja405200u http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/Oa6aJARKKwg
nmrlearner Journal club 0 09-25-2013 11:34 PM
[NMR paper] Microscopic insights into the NMR relaxation based protein conformational entropy meter.
Microscopic insights into the NMR relaxation based protein conformational entropy meter. Microscopic insights into the NMR relaxation based protein conformational entropy meter. J Am Chem Soc. 2013 Sep 6; Authors: Kasinath V, Sharp KA, Wand AJ Abstract Conformational entropy is a potentially important thermodynamic parameter contributing to protein function. Quantitative measures of conformational entropy are necessary for an understanding of its role but have been difficult to obtain. An empirical method that utilizes changes in...
nmrlearner Journal club 0 09-07-2013 09:54 PM
The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation
The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation Available online 13 December 2012 Publication year: 2012 Source:Current Opinion in Structural Biology</br> </br> Historically it has been virtually impossible to experimentally determine the contribution of residual protein entropy to fundamental protein activities such as the binding of ligands. Recent progress has illuminated the possibility of employing NMR relaxation methods to quantitatively determine the role of changes in conformational...
nmrlearner Journal club 0 02-03-2013 10:13 AM
[NMR paper] NMR relaxation studies of the role of conformational entropy in protein stability and
NMR relaxation studies of the role of conformational entropy in protein stability and ligand binding. Related Articles NMR relaxation studies of the role of conformational entropy in protein stability and ligand binding. Acc Chem Res. 2001 May;34(5):379-88 Authors: Stone MJ Recent advances in the measurement and analysis of protein NMR relaxation data have made it possible to characterize the dynamical properties of many backbone and side chain groups. With certain caveats, changes in flexibility that occur upon ligand binding, mutation, or...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] Negative entropy of halothane binding to protein: 19F-NMR with a novel cell.
Negative entropy of halothane binding to protein: 19F-NMR with a novel cell. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Negative entropy of halothane binding to protein: 19F-NMR with a novel cell. Biochim Biophys Acta. 1997 Mar 15;1334(2-3):117-22 Authors: Yoshida T, Tanaka M, Mori Y, Ueda I An obvious difficulty of the study of binding of volatile anesthetics to proteins is to prevent loss of the ligand during the procedure. A novel NMR tube was designed that...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Negative entropy of halothane binding to protein: 19F-NMR with a novel cell.
Negative entropy of halothane binding to protein: 19F-NMR with a novel cell. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Negative entropy of halothane binding to protein: 19F-NMR with a novel cell. Biochim Biophys Acta. 1997 Mar 15;1334(2-3):117-22 Authors: Yoshida T, Tanaka M, Mori Y, Ueda I An obvious difficulty of the study of binding of volatile anesthetics to proteins is to prevent loss of the ligand during the procedure. A novel NMR tube was designed that...
nmrlearner Journal club 0 08-22-2010 03:03 PM
[NMR paper] Contributions to conformational entropy arising from bond vector fluctuations measure
Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding. J Mol Biol. 1996 Oct 25;263(2):369-82 Authors: Yang D, Kay LE The relation between order parameters derived from NMR...
nmrlearner Journal club 0 08-22-2010 02:20 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 09:41 PM.


Map