Grid computing for improving conformational sampling in NMR structure calculation.
Bioinformatics. 2011 May 5;
Authors: Mareuil F, Blanchet C, Malliavin TE, Nilges M
MOTIVATION: Methods for automatic NMR structure determination need to face a high level of ambiguity encountered in NMR spectra recorded by solid-state NMR and by solution NMR of partially unfolded proteins, leading to time-consuming calculations. The software package Ambiguous Restraints for Iterative Assignment (ARIA) allows for straightforward parallelization of the calculation, as the conformers can be generated in parallel on many nodes. RESULTS: Due to its architecture, the adaptation of ARIA to grid computing can be easily achieved by using the middleware glite and JDL (Job Description Language) scripts. This adaptation makes it possible to address highly ambiguous data sets, because of the much larger conformational sampling that can be generated by use of the grid computational power. AVAILABILITY: The version 2.3.1 of ARIA implemented on the grid is freely available from the ARIA Web site: aria.pasteur.fr/downloads. CONTACT: Michael Nilges: nilges@pasteur.fr.
PMID: 21546391 [PubMed - as supplied by publisher]
A Grid-enabled web portal for NMR structure refinement with AMBER.
A Grid-enabled web portal for NMR structure refinement with AMBER.
A Grid-enabled web portal for NMR structure refinement with AMBER.
Bioinformatics. 2011 Jul 14;
Authors: Bertini I, Case DA, Ferella L, Giachetti A, Rosato A
MOTIVATION: The typical workflow for NMR structure determination involves collecting thousands of conformational restraints, calculating a bundle of 20-40 conformers in agreement with them and refining the energetics of these conformers. The structure calculation step employs simulated annealing based on molecular dynamics...
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07-16-2011 07:28 PM
[NMR paper] Automated NMR structure calculation with CYANA.
Automated NMR structure calculation with CYANA.
Related Articles Automated NMR structure calculation with CYANA.
Methods Mol Biol. 2004;278:353-78
Authors: Güntert P
This chapter gives an introduction to automated nuclear magnetic resonance (NMR) structure calculation with the program CYANA. Given a sufficiently complete list of assigned chemical shifts and one or several lists of cross-peak positions and columns from two-, three-, or four-dimensional nuclear Overhauser effect spectroscopy (NOESY) spectra, the assignment of the NOESY...
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11-24-2010 09:25 PM
[NMR paper] Protein structure calculation from NMR data.
Protein structure calculation from NMR data.
Related Articles Protein structure calculation from NMR data.
Methods Mol Biol. 2002;173:267-83
Authors: Mal TK, Bagby S, Ikura M
nmrlearner
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11-24-2010 08:49 PM
[Question from NMRWiki Q&A forum] How to keep XPLOR structure calculation from exploding?
How to keep XPLOR structure calculation from exploding?
Trying to calculate a structure using sa.inp script and the energy in the cooling loop increases instead of going down.
In the end there is a message
****&&&& rerun job with smaller timestep (i.e., 0.003)But making the timestep smaller does not help. Could anyone suggest where to look?
edit: I've also commented out my restrains thinking that maybe my noe's are too whacky, but still structure diverges.
nmrlearner
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11-02-2010 11:22 PM
[NMR paper] Conformational sampling by NMR solution structures calculated with the program DIANA
Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water.
Related Articles Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water.
Proteins. 1996 Mar;24(3):304-13
Authors: Berndt KD, Güntert P, Wüthrich K
The NMR solution structure of bovine pancreatic trypsin inhibitor (BPTI) obtained by distance geometry...
protein structure calculation
Hi! every one!
I wanted to get in contact with people solving the structure of protein by using NMR. I am learning the process and i have many basics problem related with the work.
cheers!
Grid computing for improving conformational sampling in NMR structure calculation.
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