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 09-24-2010, 04:57 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,652
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 MOBI: a web server to define and visualize structural mobility in NMR protein ensembl

MOBI: a web server to define and visualize structural mobility in NMR protein ensembles.

Related Articles MOBI: a web server to define and visualize structural mobility in NMR protein ensembles.

Bioinformatics. 2010 Sep 21;

Authors: Martin AJ, Walsh I, Tosatto SC

MOTIVATION: MOBI is a web server for the identification of structurally mobile regions in NMR protein ensembles. It provides a binary mobility definition that is analogous to the commonly used definition of intrinsic disorder in X-ray crystallographic structures. At least three different use cases can be envisaged: (i) Visualization of NMR mobility for structural analysis; (ii) definition of regions for reliable comparative modelling in protein structure prediction; (iii) definition of mobility in analogy to intrinsic disorder. MOBI uses structural superposition and local conformation differences to derive a robust binary mobility definition that is in excellent agreement with the manually curated definition used in the CASP8 experiment for intrinsic disorder in NMR structure. The output includes mobility-coloured PDB files, mobility plots and a FASTA formatted sequence file summarizing the mobility results. AVAILABILITY: The MOBI server and supplementary methods are available for non-commercial use at URL: http://protein.bio.unipd.it/mobi/.

PMID: 20861031 [PubMed - as supplied by publisher]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[KPWU blog] [web server] protein structural analysis
protein structural analysis PDBsum provides service that users can upload their calculated structures for analysis including ramachandran plot, sequence+secondary structural element, etc. The figure below is an example. For self-generated structures, users need to click the link “generate” to upload your PDB files. To know the structural information of published biomolecules at Protein Data Bank, just type the http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=570&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.
nmrlearner News from NMR blogs 0 10-12-2011 06:37 AM
[NMR paper] Structural mobility of the extracellular ligand-binding core of an ionotropic glutama
Structural mobility of the extracellular ligand-binding core of an ionotropic glutamate receptor. Analysis of NMR relaxation dynamics. Related Articles Structural mobility of the extracellular ligand-binding core of an ionotropic glutamate receptor. Analysis of NMR relaxation dynamics. Biochemistry. 2002 Aug 20;41(33):10472-81 Authors: McFeeters RL, Oswald RE Ionotropic glutamate receptors play important roles in a variety of neuronal processes and have been implicated in multiple neurodegenerative diseases. The extracellular ligand-binding...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] Residue-specific real-time NMR diffusion experiments define the association states of
Residue-specific real-time NMR diffusion experiments define the association states of proteins during folding. Related Articles Residue-specific real-time NMR diffusion experiments define the association states of proteins during folding. J Am Chem Soc. 2002 Jun 19;124(24):7156-62 Authors: Buevich AV, Baum J Characterizing the association states of proteins during folding is critical for understanding the nature of protein-folding intermediates and protein-folding pathways, protein aggregation, and disease-related aggregation. To study the...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] A solid-state NMR study of protein mobility in lyophilized protein-sugar powders.
A solid-state NMR study of protein mobility in lyophilized protein-sugar powders. Related Articles A solid-state NMR study of protein mobility in lyophilized protein-sugar powders. J Pharm Sci. 2002 Apr;91(4):943-51 Authors: Lam YH, Bustami R, Phan T, Chan HK, Separovic F The molecular mobility of protein in lyophilized lysozyme-sugar systems stored at different relative humidities was studied using solid-state NMR. Relaxation measurements, T(1) of high-frequency (MHz), and T(1rho), of low-frequency (kHz) motions, were performed on lysozyme...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[BMNRC community] The PSIPRED Protein Structure Prediction Server
The PSIPRED Protein Structure Prediction Server http://bioinf.cs.ucl.ac.uk/psipred/ Go to BMNRC community to find more info about this topic.
nmrlearner News from other NMR forums 0 09-04-2010 06:53 AM
[NMR paper] Loop mobility in a four-helix-bundle protein: 15N NMR relaxation measurements on huma
Loop mobility in a four-helix-bundle protein: 15N NMR relaxation measurements on human interleukin-4. Related Articles Loop mobility in a four-helix-bundle protein: 15N NMR relaxation measurements on human interleukin-4. Biochemistry. 1992 Nov 3;31(43):10431-7 Authors: Redfield C, Boyd J, Smith LJ, Smith RA, Dobson CM 15N NOE, T1, and T2 measurements have been carried out on uniformly 15N-labeled human interleukin-4. Analysis of the results in terms of order parameters (S2) shows that although the helical core of this four-helix-bundle protein...
nmrlearner Journal club 0 08-21-2010 11:45 PM
PECAN server - protein secondary structure via NMR
http://bija.nmrfam.wisc.edu/PECAN/Pecan.jpg Link to the PECAN server Instructions about PECAN input files Info from the PECAN website:PECAN offers a new approach to secondary structure identification that achieves excellent results. PECAN is a component in a suite of tools for high-throughput structure determination using NMR.
nmrlearner NMR software 0 07-20-2005 05:44 PM
PISTACHIO - autoassignment server for protein NMR
http://www.bionmr.com/forum/style_images/pistachio_small.jpg Link to the PISTACHIO Server Input instructions Info from the PISTACHIO website:PISTACHIO offers fully automatic backbone and sidechain assignments using a new approach to assignment that achieves excellent results. PISTACHIO is a component in a suite of tools for high-throughput structure determination using NMR.
nmrlearner NMR software 0 07-20-2005 05:25 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 05:21 PM.


Map