A Fast Pocket Extraction and Evaluation for Protein Surfaces

Research of protein is pivotal to the drug discovery, since most of the drugs act upon proteins inside human body. Drugs act when they are close to the concave portions, so called “pockets”, of protein surfaces. Therefore, detection and analysis of the pockets are also important for the drug discovery. This paper presents a fast pocket extraction and evaluation technique for protein surfaces. Supposing protein surfaces are provided as triangular meshes, the method first applies mesh simplification to smooth small geometric features. It then detects concave portions from the simplified triangular meshes as pockets. The method then evaluates the pockets from the following viewpoints: geometric evaluation and chemical evaluation.