Biomolecules molecular modeling

Combining 2D-NOESY and 2D-ROESY NMR experiments with molecular modelling protocols, Kuhn and Kunz32 have been able to study the saccharide-induced peptide conformational behaviour of the recognition region of Ll-Cadherin. The detailed conformational analysis of this key biomolecule not only proves that the saccharide side chain exerts a marked influence on the conformation of the peptide chain, but also that the size and type of the saccharide indeed strongly affects the conformation of the main chain. 

Molecular modeling Computer programs that allow the visualization of the structure of a biomolecule and the modeling of their properties Used to investigate the properties of biomolecules when experimental techniques can not be used... 

Published FF parameters for MM (Jalaie and Lipkowitz, 2000 Osawa and Lip-kowitz, 1995) and software for molecular modeling (Boyd, 1995) have been compiled. Some of the MM programs applicable to molecular modeling of biomolecules are listed in Table 14.1. 

The 3D space requirements of most molecules can be represented to a good approximation by such Van der Waals surfaces. Fused sphere VDWS s are used extensively in molecular modeling, especially in the interpretation of biochemical processes and computer aided drug design. These approximate molecular surfaces are conceptually simple, their computation and graphical display on a computer screen take relatively short time, even for large biomolecules. 

The emergence of molecular modeling and computational into a discipline has been closely associated with advances in computer hardware, computer graphics, and software. The availability of more sophisticated number-crunching power has allowed scientists to calculate the properties oflarger and larger molecules. With the advent of supercomputers, dynamics calculations on biomolecules surrounded by an environment of water are becoming common. 

Computer-based molecular modelling is finding application in the study of biomolecules and their interactions. 

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