Molecular field feature extraction and analysis with level set method

In this paper, we exploit the level set methods to extract and analyze the feature of macromolecular field. For the 3D volume data of the field, we propose a novel variational formulation of the geometric active contour, which is composed of an external energy to drive the active contour, and an internal energy which penalizes the level set function adaptively to avoid periodically re-initializing. We adjust the parameters of each component and examine their influences in the whole process. Our approach provides an intuitive way to study spatial relationships of the segmented regions. Compared with the traditional level set frameworks, our approach is more accurate and efficient on the feature extraction regarding the HIV-1 protease molecular field and the DPS protein molecular field. During the exploration, we successfully found the escape route of water molecules hidden in the HIV-1 protease and the internal cavity of the DPS protein for the iron atom's entry and deposition. Both of these results support the experimental results given by chemists and biologists.