Journal ArticleDOI
Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry
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This article is published in ChemInform.The article was published on 1990-11-20. It has received 44 citations till now.read more
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Prediction of protein-ligand interactions. Docking and scoring: successes and gaps.
TL;DR: The area of calculating molecular interactions, specifically docking, the positioning of a ligand in a protein binding site, and scoring, the quality assessment of docked ligands is called attention.
Journal ArticleDOI
Dynamics of biochemical and biophysical reactions: insight from computer simulations.
Arieh Warshel,William W. Parson +1 more
TL;DR: Experimental studies of biological processes such as photoisomerization and electron transfer have provided a wealth of detailed information that eventually may make some of these processes classical problems in chemical physics as well as biology.
Journal ArticleDOI
On the truncation of long-range electrostatic interactions in DNA.
Jan Norberg,Lennart Nilsson +1 more
TL;DR: To perform accurate and stable simulations of highly charged biological macromolecules, it is recommended that the atom-based force-shift method or the PME method should be used for the long-range electrostatics interactions.
Journal ArticleDOI
Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data
TL;DR: This comprehensive benchmark based on NMR data applied to many popular MD force fields is presented, finding that for gb3, the force-field AMBER99sb reaches comparable accuracy in back-calculated residual dipolar couplings and J-couplings across hydrogen bonds to ensembles obtained by refinement against N MR data.
Journal ArticleDOI
Interaction of the Disaccharide Trehalose with a Phospholipid Bilayer: A Molecular Dynamics Study
Cristina Silva Pereira,Roberto D. Lins,Indira Chandrasekhar,Luiz C. G. Freitas,Philippe H. Hünenberger +4 more
TL;DR: In this study, molecular dynamics simulations are used to investigate the interaction of trehalose with a phospholipid bilayer at atomistic resolution and show that trehalOSE is able to minimize the disruptive effect of the elevated temperature and stabilize the bilayer structure.
References
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Journal ArticleDOI
Moleküldynamik‐Computersimulationen; Methodik, Anwendungen und Perspektiven in der Chemie
TL;DR: In this article, the authors present an approach for the simulation of Molekuldynamik (MD)-Simulation systems with a computer, in which the Molekulare Modell and the Rechenvorgang are treffen, das ihre jeweiligen Beitrage zur Gesamtungenauigkeit von ahnlicher Grose sind, ohne dabei die interessierende Systemeigenschaft signifikant zu beeinflussen.