BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Software > Molecular modeling software > NMR dynamics
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 Rating: Thread Rating: 1 votes, 4.00 average. Display Modes
  #1  
Unread 03-14-2005, 09:45 AM
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

Links

Tensor 2 download

Tensor 2 manual

Tensor 2 theory


Description of the program from the Tensor website:

TENSOR2 allows the determination of the rotational diffusion tensor from three-dimensional structure coordinates and 15N relaxation data. Confidence in the various models available to describe the tensor is estimated using Monte-Carlo sampling methods in combination with appropriate kai^2 and F-tests, made possible by a highly efficient simulated annealing algorithm.

A graphical interface allows the visualisation of the orientation of tensorial components with respect to the three-dimensional coordinates of the molecule, and provides a graphical presentation of the statistical behaviour of the system.

Tensor now carries out an analysis of internal motion using the Lipari-Szabo or extended Lipari-Szabo type analysis. It's about time. This can either be performed using an isotropic rotor to describe rotational diffusion, or using the anisotropic tensor determined using a subset of spins, themselves assumed to have a negligible component to their internal motion. The internal mobility analysis is performed using the logic introduced by the NIH lab (Clore et al 1990),and reproduced by Professor Art Palmer's lab (Mandel et al 1995), sequentially fitting with more complicated models until the data are adequately reproduced. The confidence limits and uncertainty in the parameters are determined using a rapid monte-carlo based statistical analysis. As has been noted by numerous authors, the error function defined by the fitted internal mobility parameters {S2,ti} is highly non-linear when fitting R1,R2 and heteronuclear nOe. It is now possible to rapidly scan the monte-carlo simulations from the fit of each 15N site to check the definition of the optimised internal mobility parameters."
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes.
Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes. Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes. Amino Acids. 2011 Apr 9; Authors: Hu M, Li Y, Yang G, Li G, Li M, Wen Z Internal motions and flexibility are essential for biological functions in proteins. To assess the internal fluctuations and conformational flexibility of proteins, reliable computational methods are needed. In this study, wavelet transformation was used to filter out the noise and...
nmrlearner Journal club 0 04-12-2011 11:08 AM
Analysis of the amide 15N chemical shift tensor of the Cα tetrasubstituted constituent of membrane-active peptaibols, the α-aminoisobutyric acid residue, compared to those of di- and tri-substituted proteinogenic amino acid residues
Analysis of the amide 15N chemical shift tensor of the Cα tetrasubstituted constituent of membrane-active peptaibols, the α-aminoisobutyric acid residue, compared to those of di- and tri-substituted proteinogenic amino acid residues <div class="Abstract">Abstract In protein NMR spectroscopy the chemical shift provides important information for the assignment of residues and a first structural evaluation of dihedral angles. Furthermore, angular restraints are obtained from oriented samples by solution and solid-state NMR spectroscopic approaches. Whereas the anisotropy of chemical...
nmrlearner Journal club 0 01-09-2011 12:46 PM
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1.
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1. NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1. Biochemistry. 2011 Jan 4; Authors: Parkesh R, Disney MD, Fountain M The NMR structure of an RNA with a copy of the 5'CUG/3'GUC motif found in the triplet repeating disorder myotonic dystrophy type 1 (DM1) is disclosed. The lowest energy conformation of the UU pair is a single...
nmrlearner Journal club 0 01-06-2011 11:21 AM
[NMR paper] Correlation of binding-loop internal dynamics with stability and function in potato I
Correlation of binding-loop internal dynamics with stability and function in potato I inhibitor family: relative contributions of Arg(50) and Arg(52) in Cucurbita maxima trypsin inhibitor-V as studied by site-directed mutagenesis and NMR spectroscopy. Related Articles Correlation of binding-loop internal dynamics with stability and function in potato I inhibitor family: relative contributions of Arg(50) and Arg(52) in Cucurbita maxima trypsin inhibitor-V as studied by site-directed mutagenesis and NMR spectroscopy. Biochemistry. 2002 Jul 30;41(30):9572-9 ...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] Slow internal dynamics in proteins: application of NMR relaxation dispersion spectros
Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme. Related Articles Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme. J Am Chem Soc. 2002 Feb 20;124(7):1443-51 Authors: Mulder FA, Hon B, Mittermaier A, Dahlquist FW, Kay LE Recently developed carbon transverse relaxation dispersion experiments (Skrynnikov, N. R.; et al. J. Am. Chem. Soc. 2001, 123, 4556-4566) were...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] Influence of internal dynamics on accuracy of protein NMR structures: derivation of r
Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory. Related Articles Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory. J Mol Biol. 1999 Jan 15;285(2):727-40 Authors: Schneider TR, Brünger AT, Nilges M In order to study the effect of internal dynamics on the accuracy of NMR structures in detail, we generated NOE distance data from a...
nmrlearner Journal club 0 11-18-2010 07:05 PM
[NMR paper] NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding reg
NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor (CMTI)-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. Related Articles NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor (CMTI)-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. ...
nmrlearner Journal club 0 11-17-2010 11:06 PM
[NMR paper] Assignment of 13C resonances and analysis of relaxation properties and internal dynam
Assignment of 13C resonances and analysis of relaxation properties and internal dynamics of pike parvalbumin by 13C-NMR at natural abundance. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Assignment of 13C resonances and analysis of relaxation properties and internal dynamics of pike parvalbumin by 13C-NMR at natural abundance. Eur J Biochem. 1996 May 1;237(3):561-74 Authors: Alattia T, Padilla A, Cavé A Pike parvalbumin is an...
nmrlearner Journal club 0 08-22-2010 02:27 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 11:50 AM.


Map