Journal ArticleDOI
Geometry Optimization of Carbohydrate Binding Sites of Influenza: A Quantum Mechanical Approach
Veeramani Murugan,Ponnusamy Parasuraman,Jeyasigamani F. A. Selvin,Thanu R. K. Priyadarzini,M. Michael Gromiha,Kazuhiko Fukui,K. Veluraja +6 more
TLDR
In this paper, an algorithm to generate input files for quantum mechanical (QM) calculations from molecular dynamics trajectories of protein-carbohydrate complex simulations and QM optimization of binding-site residues of influenza hemagglutinin H1 along with its cell surface receptor sialyldisaccharides Neu5Acα(2→3)Gal (N23G) and Neu 5Acα (2→6)Gal(N26G).About:
This article is published in Journal of Carbohydrate Chemistry.The article was published on 2015-10-22. It has received 3 citations till now.read more
Citations
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Essentials Of Computational Chemistry Theories And Models
TL;DR: “Essentials” covers force field and molecular orbital theory, Monte Carlo and Molecular Dynamics simulations, thermodynamic and electronic (spectroscopic) property calculation, condensed phase treatment and a few more topics, and is an alternative to Andrew R. Leach's well-established “Molecular Modeling” and Frank Jensen’s “Introduction to Computational Chemistry”.
Journal ArticleDOI
Theoretical investigation on the binding specificity of fluorinated sialyldisaccharides Neu5Acα(2–3)Gal and Neu5Acα(2–6)Gal with influenza hemagglutinin H1 – A Molecular Dynamics Study
Veeramani Murugan,Ponnusamy Parasuraman,Jeyasigamani F. A. Selvin,M. Michael Gromiha,Kazuhiko Fukui,K. Veluraja +5 more
TL;DR: It was concluded that FN26G should be a better binder for hemagglutinin (H1) than FN23G and it might act as an inhibitor for influenza.
Journal ArticleDOI
Design of fluorinated sialic acid analog inhibitor to H5 hemagglutinin of H5N1 influenza virus through molecular dynamics simulation study.
TL;DR: This study suggests that one can design the inhibitor by using the mono fluorinated models SIA-F9, Sia-F2 and SIA -F7 and difluorinated modelsSIA-f2F4, SIA’F2F9 and S IA-F7F9 to inhibit H5 of H5N1 to avoid Influenza A viral infection.
References
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Journal ArticleDOI
A simplex method for function minimization
John A. Nelder,R. Mead +1 more
TL;DR: A method is described for the minimization of a function of n variables, which depends on the comparison of function values at the (n 41) vertices of a general simplex, followed by the replacement of the vertex with the highest value by another point.
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Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint
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MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
TL;DR: The MOLSCRIPT program as discussed by the authors produces plots of protein structures using several different kinds of representations, including simple wire models, ball-and-stick models, CPK models and text labels.
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Natural population analysis
TL;DR: In this paper, a method of "natural population analysis" was developed to calculate atomic charges and orbital populations of molecular wave functions in general atomic orbital basis sets, which seems to exhibit improved numerical stability and to better describe the electron distribution in compounds of high ionic character.