Study of conformational properties of a biologically active peptide of fibronectin by circular dichroism, NMR and molecular dynamics simulation

2006 ◽  
Vol 8 (40) ◽  
pp. 4668 ◽  
Author(s):  
Sergio Abbate ◽  
Sergio Barlati ◽  
Marina Colombi ◽  
Sandro L. Fornili ◽  
Pierangelo Francescato ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Molecular Dynamics Simulation ◽  
Biologically Active ◽  
Dynamics Simulation ◽  
Active Peptide ◽  
Conformational Properties ◽  
Biologically Active Peptide ◽  
Circular Dichroïsm

Calculation of the circular dichroism spectrum of cyclo(l-tyr-l-tyr) based on a molecular dynamics simulation

1994 ◽  
Vol 49 (2) ◽  
pp. 141-152 ◽  
Author(s):  
Jörg Fleischhauer ◽  
Joachim Grötzinger ◽  
Bernd Kramer ◽  
Peter Krüger ◽  
Axel Wollmer ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Molecular Dynamics Simulation ◽  
Circular Dichroism Spectrum ◽  
Dynamics Simulation ◽  
Circular Dichroïsm

Conformational study of bovine lactoferricin in membrane-micking conditions by molecular dynamics simulation and circular dichroism

BioMetals ◽  
2010 ◽  
Vol 24 (2) ◽  
pp. 259-268 ◽  
Author(s):  
Isabella Daidone ◽  
Alessandro Magliano ◽  
Alfredo Di Nola ◽  
Giuseppina Mignogna ◽  
Matilda Manuela Clarkson ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Conformational Study ◽  
Bovine Lactoferricin ◽  
Circular Dichroïsm

Conformational studies of a benzodiazepine-like peptide in SDS micelles by circular dichroism,1H NMR and molecular dynamics simulation

1997 ◽  
Vol 4 (4-6) ◽  
pp. 359-364 ◽  
Author(s):  
Marc Lecouvey ◽  
Céline Frochot ◽  
Laurent Miclo ◽  
Piotr Orlewski ◽  
Michel Marraud ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Molecular Dynamics Simulation ◽  
1H Nmr ◽  
Dynamics Simulation ◽  
Conformational Studies ◽  
Sds Micelles ◽  
Circular Dichroïsm

scholarly journals Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation

Molecules ◽  
2020 ◽  
Vol 25 (9) ◽  
pp. 2196
Author(s):  
Barış Kurt ◽  
Hamdi Temel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ab Initio ◽  
Biologically Active ◽  
Dynamics Simulation ◽  
The Novel ◽  
Ab Initio Method ◽  
Crystallographic Structures ◽  
Dynamics Simulations ◽  
Experimental Structure

Boric acid, borate esters, and hydroxy derivatives are biologically active molecules. Thus, performing molecular dynamics simulations of these molecules is vital in terms of drug design, but it is difficult to find directly generated Amber parameters based on an ab initio method for these kinds of molecules in the literature. In this study, Amber parameters for such molecules containing boron were generated based on ab initio calculations using the paramfit program, which applies a combination of genetic and simplex algorithms, and the Visual Force Field Derivation Toolkit (VFFDT) program containing the Seminario method. The minimized structure, after obtaining novel parameters and using the sander program, was compared with the experimental crystallographic structures, and it was observed that the root-mean-square deviation (RMSD) value between the experimental structure and minimized structure agreed reasonably well. In addition, the molecule was heated, and the molecular dynamics simulation was successfully obtained with the novel parameters.

Conformational and Dynamic Properties of Polymer Loops and Their Mixtures at an Impenetrable Interface

1996 ◽  
Vol 463 ◽  
Author(s):  
H. S. Gulati ◽  
D. C. Driscoll ◽  
R. L. Jones ◽  
R. J. Spontak ◽  
C. K. Hall
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamic Properties ◽  
Relaxation Behavior ◽  
Dynamics Simulation ◽  
Dynamic Relaxation ◽  
Conformational Properties ◽  
Fluctuation Method ◽  
Bond Fluctuation ◽  
The Individual

ABSTRACTIn this study we investigate the equilibrium conformational properties and dynamic relaxation behavior of polymer loops grafted at an interface using the discontinuous molecular dynamics simulation technique. Differences and similarities between the structural and dynamic properties of polymer loops and tails are identified. The conformational properties of mixtures of polymers loops and tails are also studied using the bond-fluctuation method. The effect of mixture composition on the conformational properties of the individual components in the mixture is discussed.

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