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 (MD) simulations with very simplified force fields. The value of refining the calculated conformers using restrained MD (rMD) simulations with state-of-art force fields is documented. This refinement however presents various subtleties, from the proper formatting of conformational restraints to the definition of suitable protocols. RESULTS: We describe a web interface to set up and run calculations with the AMBER package, which we called AMPS-NMR (AMBER- based Portal Server for NMR structures). The interface allows the refinement of NMR structures through rMD. Some predefined protocols are provided for this purpose, which can be personalized; it is also possible to create an entirely new protocol. AMPS-NMR can handle various restraint types. Standard rMD refinement in explicit water of the structures of an all-helical and an all-beta protein are shown as examples. AMPS-NMR additionally includes a workspace for the user to store different calculations. As an ancillary service, a web interface to AnteChamber is available, enabling the calculation of force field parameters for organic molecules such as ligands in protein-ligand adducts. Availability and Implementation: AMPS-NMR is embedded within the NMR services of the WeNMR project and is available at http://py-enmr.cerm.unifi.it/access/index/amps-nmr; its use requires registration with a digital certificate. CONTACT: ivanobertini@cerm.unifi.it SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.
PMID: 21757462 [PubMed - as supplied by publisher]
Grid computing for improving conformational sampling in NMR structure calculation.
Grid computing for improving conformational sampling in NMR structure calculation.
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...
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[NMR paper] An AMBER/DYANA/MOLMOL phosphorylated amino acid library set and incorporation into NMR structure calculations.
An AMBER/DYANA/MOLMOL phosphorylated amino acid library set and incorporation into NMR structure calculations.
Related Articles An AMBER/DYANA/MOLMOL phosphorylated amino acid library set and incorporation into NMR structure calculations.
J Biomol NMR. 2005 Sep;33(1):15-24
Authors: Craft JW, Legge GB
Protein structure determination using Nuclear Magnetic Resonance (NMR) requires the use of molecular dynamics programs that incorporate both NMR experimental and implicit atomic data. Atomic parameters for each amino acid type are encoded in...
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12-01-2010 06:56 PM
[NMR paper] Object-oriented approach to drug design enabled by NMR SOLVE: first real-time structu
Object-oriented approach to drug design enabled by NMR SOLVE: first real-time structural tool for characterizing protein-ligand interactions.
Related Articles Object-oriented approach to drug design enabled by NMR SOLVE: first real-time structural tool for characterizing protein-ligand interactions.
J Cell Biochem Suppl. 2001;Suppl 37:99-105
Authors: Sem DS, Yu L, Coutts SM, Jack R
As a result of genomics efforts, the number of protein drug targets is expected to increase by an order of magnitude. Functional genomics efforts are identifying...
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[BMNRC community] HADDOCK Software web portal
HADDOCK Software web portal
http://haddock.chem.uu.nl/index.html
Go to BMNRC community to find more info about this topic.
Gorenstein's scripts for Amber, etc.
The following Perl scripts for Amber-driven NMR structure determination are available from the website of Dr. Gorenstein:carnal.aveminclusters.in Calculates the average structure from sander restrt files and
calculates the RMSD for each vs. the average structure.
addcio.pl Add Na+ counterions to DNA
amber_2_charm.pl
amber_dna_pdb_to_star.pl
amber_pdb_to_star.pl
A Grid-enabled web portal for NMR structure refinement with AMBER.
Linear Mode
