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Molecular Fourier Transformation - Biomatics.org

Molecular Fourier Transformation

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J Comput Chem. 2010 Feb;31(3):649-59.

Fourier transform convolution integrals applied to generalized Born molecular volume.


Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland. thierry.schuepbach@isb-sib.ch


Generalized Born methods are currently among the solvation models most commonly used for biological applications. We reformulate the generalized Born molecular volume method initially described by (Lee et al, 2003, J Phys Chem, 116, 10606; Lee et al, 2003, J Comp Chem, 24, 1348) using fast Fourier transform convolution integrals. Changes in the initial method are discussed and analyzed. Finally, the method is extensively checked with snapshots from common molecular modeling applications: binding free energy computations and docking. Biologically relevant test systems are chosen, including 855-36091 atoms. It is clearly demonstrated that, precision-wise, the proposed method performs as good as the original, and could better benefit from hardware accelerated boards.

Copyright 2009 Wiley Periodicals, Inc.

[PubMed - indexed for MEDLINE]

Topological study of intramolecular hydrogen bonding in -hydroxyethylperoxy radical and -hydroxyethoxy radical along its dissociation pathway
Marcos Mandado, Ricardo A. Mosquera and Christian Van Alsenoy,  Phys. Chem. Chem. Phys., 2005, 7, 3290
DOI: 10.1039/b507300f

graphical abstract image (ID: b507300f)

QTAIM calculations indicate that intramolecular hydrogen bond is present in -hydroxyethylperoxy but not in -hydroxyethoxy radical.

Structure, dipole moment and large amplitude motions of 1-benzofuran
Assimo Maris, B. Michela Giuliano, Sonia Melandri, Paolo Ottaviani, Walther Caminati, Laura B. Favero and Biagio Velino,  Phys. Chem. Chem. Phys., 2005, 7, 3317
DOI: 10.1039/b507795h

graphical abstract image (ID: b507795h)

Several molecular properties of 1-benzofuran are reported. The molecular beam Fourier transform 414–303 transition of the 13C(5) isotopomer is graphically presented.


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