{'fraction_non_alphanumeric': 0.025678650036683785, 'fraction_numerical': 0.001467351430667645, 'mean_word_length': 5.464454976303317, 'pattern_counts': {'":': 0, '<': 0, '<?xml version=': 0, '>': 0, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
An accelerated pocket extraction and evaluation technique for druggability analysis with protein surfaces

Drugs act upon the concave portions of protein surfaces, so called "pockets". Discovery of well-shaped pockets on protein surfaces is an active research topic. Several survey papers in this field report many methods to search druggable pockets, which can be divided in two major categories: geometric algorithms and/or energy-based methods. There are varieties of method-dependent geometric descriptions of binding pockets such as depth, size, volume, and amino acid composition, because there are no standard definitions of what constitutes a pocket. We had a discussion with specialists of drug discovery, and received the following suggestions: (1) It should be reasonable to eliminate proteins which do not have well-shaped pockets, before the chemical and energetic analysis phase. (2) It is desirable to develop techniques that roughly but quickly discover well-shaped pockets. Based on the discussion, this paper presents a quick pocket extraction and evaluation technique. It applies a mesh simplification technique to protein surfaces, extracts concave portions from the simplified surfaces, and projects the portions to the original surfaces. Finally, it evaluates the shapes of the portions by comparing with preferably evaluated sample pockets.