Abstract
The different surfaces usually defined in molecular modeling are explored focusing the attention on comparing the two common surfaces which incorporate the presence of the solvent: the Accessibility Molecular Surface (AMS) and the Richards Molecular Surface (RMS). The information contained in these surfaces is analyzed by studying the changes associated to the systematic variation of the radius of the solvent, represented by a probe sphere. An approximation to the effective fractal dimension associated with the RMS is also obtained. Four biomolecules, hyaluronic acid (HYA) and three proteins, crambin (CRN), lysozyme (LYZ), and thaumatin-I (THI), with sizes ranging from around 100 to 1500 atoms, have been chosen for this study. Graphical ray-traced renderings of these biomolecules, obtained by adapting public domain ray-tracing software are presented.
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