Abstract For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, 3 J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.
Content Type Journal Article
Category Article
Pages 1-17
DOI 10.1007/s10858-011-9534-0
Authors
Nathan Schmid, Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
Jane R. Allison, Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
Jožica Dolenc, Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
Andreas P. Eichenberger, Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
Anna-Pitschna E. Kunz, Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
Wilfred F. van Gunsteren, Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
[CNS Yahoo group] water refinement problem - broken structure
water refinement problem - broken structure
Dear all, I'm trying to perform water refinement for the very first time (new CNS user), on an NMR ensemble of CYANA calculated protein structures but the end
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nmrlearner
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07-18-2011 09:41 AM
Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation.
Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation.
Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation.
Biophys J. 2010 Nov 17;99(10):3282-9
Authors: Toraya S, Javkhlantugs N, Mishima D, Nishimura K, Ueda K, Naito A
Bombolitin II (BLT2) is one of the hemolytic heptadecapeptides originally isolated from the venom of a bumblebee. Structure and orientation of BLT2 bound to...
nmrlearner
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03-03-2011 12:34 PM
The structure of the talin/integrin complex at a lipid bilayer: an NMR and MD simulation study.
The structure of the talin/integrin complex at a lipid bilayer: an NMR and MD simulation study.
The structure of the talin/integrin complex at a lipid bilayer: an NMR and MD simulation study.
Structure. 2010 Oct 13;18(10):1280-8
Authors: Kalli AC, Wegener KL, Goult BT, Anthis NJ, Campbell ID, Sansom MS
Integrins are cell surface receptors crucial for cell migration and adhesion. They are activated by interactions of the talin head domain with the membrane surface and the integrin ? cytoplasmic tail. Here, we use coarse-grained molecular dynamic...
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03-03-2011 12:34 PM
[NMR paper] Essential spaces defined by NMR structure ensembles and molecular dynamics simulation
Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap.
Related Articles Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap.
Proteins. 1998 Jun 1;31(4):370-82
Authors: Abseher R, Horstink L, Hilbers CW, Nilges M
Large concerted motions of proteins which span its "essential space," are an important component of protein dynamics. We investigate to what extent structure ensembles generated with standard structure calculation...
nmrlearner
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11-17-2010 11:06 PM
[CNS Yahoo group] refinement of large low resolution structure
refinement of large low resolution structure
Hi all, I have a structure at 2.65A that I'm in the process of refining. It's a complex that has ~1100 residues total, and what looks like a fair amount of
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nmrlearner
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10-22-2010 07:36 PM
[NMR paper] NMR chemical shifts and structure refinement in proteins.
NMR chemical shifts and structure refinement in proteins.
Related Articles NMR chemical shifts and structure refinement in proteins.
J Biomol NMR. 1993 Sep;3(5):607-12
Authors: Laws DD, de Dios AC, Oldfield E
Computation of the 13C alpha chemical shifts (or shieldings) of glycine, alanine and valine residues in bovine and Drosophila calmodulins and Staphylococcal nuclease, and comparison with experimental values, is reported using a gauge-including atomic orbital quantum-chemical approach. The full approximately 24 ppm shielding range is...
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08-22-2010 03:01 AM
structure refinement after cyana
Can anybody tell me, how to energy minimize a CYANA calculated average structure. I used model_minimize.inp from CNS, but is there any other method generally used by the CYANA users.
Also, how can I get the bonds, impropers and angle violation (rmsds) information on the CYANA calculated structures. Does CYANA has any program to do it.
Please help me with it.
Thank you.
sarun
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11-20-2008 03:41 AM
Structure refinement based on adaptive restraints using local-elevation simulation
Biomolecular structure refinement based on adaptive restraints using local-elevation simulation
Markus Christen, Bettina Keller and Wilfred F. van Gunsteren
Journal of Biomolecular NMR; 2007; 39(4) pp 265 - 273
Abstract:
Introducing experimental values as restraints into molecular dynamics (MD) simulation to bias the values of particular molecular properties, such as nuclear Overhauser effect intensities or distances, dipolar couplings, 3 J-coupling constants, chemical shifts or crystallographic structure factors, towards experimental values is a widely used structure refinement...
Biomolecular structure refinement using the GROMOS simulation software
Linear Mode
