Protein structural models, usage

Charge transfer (CT) and proton transport are very precisely tuned due to a protein structure. Such CT processes in photosynthetic complexes may be effectively modeled using both quantum and classical method (Buda 2009). Proton translocations in proteins are well followed by computer simulations (Cukier 2004). An application of the MD methods in studies of biomimetic complexes having some prospective usage in bionanotechnology has been published (Alvarez-Paggi et al. 2010). 

Abstract The present knowledge of protein science includes information on amino acid sequence and 3D structure in terms of precise models on the atomic level. Recourse to the respective databanks and advanced computer programs allows a series of molecular features to be calculated. Application of analytical surface calculation programs (SIMS, MSRoU) based on atomic coordinates or the coordinates of gravity centers of amino acids allows precise molecular dot surfaces to be calculated, in addition to numerical data for anhydrous molecular surface and anhydrous molecular volume. Usage of in-house hydration programs (HY-DCRYST, HYDMODEL) permits the putative localization of individual water molecules on the protein envelope to be addressed explicitly. To estimate the overall values of protein volume and hydration, simple approximations based on the amino acid composition and characteristic numbers for the constituents can be used. Derivation of secondary... 

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