Related ArticlesMOBI: 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]
[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.
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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
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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...
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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...
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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.
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News from other NMR forums
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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...
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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.
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NMR software
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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.
MOBI: a web server to define and visualize structural mobility in NMR protein ensembl
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