Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey

• Published in: Computer graphics forum 2017-12, Vol.36 (8), p.643-683
• Main Authors: Simões, Tiago, Lopes, Daniel, Dias, Sérgio, Fernandes, Francisco, Pereira, João, Jorge, Joaquim, Bajaj, Chandrajit, Gomes, Abel
• Format: Article
• Language: English
• Subjects: Algorithms; Biological activity; biological modelling; computational geometry; Evolutionary algorithms; Geometric algorithms; geometric modelling; Graphics processing units; Grooves; Holes; I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling; I.3.8 [Computer Graphics]: Applications – Molecular Graphics; J.3 [Life and Medical Sciences]: Biology and Genetics – Computational Biology; modelling; Proteins; Taxonomy; Tessellation; Three dimensional models
• ISSN: 0167-7055; 1467-8659
• DOI: 10.1111/cgf.13158

Detecting and analysing protein cavities provides significant information about active sites for biological processes (e.g. protein–protein or protein–ligand binding) in molecular graphics and modelling. Using the three‐dimensional (3D) structure of a given protein (i.e. atom types and their locations in 3D) as retrieved from a PDB (Protein Data Bank) file, it is now computationally viable to determine a description of these cavities. Such cavities correspond to pockets, clefts, invaginations, voids, tunnels, channels and grooves on the surface of a given protein. In this work, we survey the literature on protein cavity computation and classify algorithmic approaches into three categories: evolution‐based, energy‐based and geometry‐based. Our survey focuses on geometric algorithms, whose taxonomy is extended to include not only sphere‐, grid‐ and tessellation‐based methods, but also surface‐based, hybrid geometric, consensus and time‐varying methods. Finally, we detail those techniques that have been customized for GPU (graphics processing unit) computing. Detecting and analysing protein cavities provides significant information about active sites for biological processes (e.g. protein–protein or protein–ligand binding) in molecular graphics and modelling. Using the three‐dimensional (3D) structure of a given protein (i.e. atom types and their locations in 3D) as retrieved from a PDB (Protein Data Bank) file, it is now computationally viable to determine a description of these cavities. Such cavities correspond to pockets, clefts, invaginations, voids, tunnels, channels and grooves on the surface of a given protein. In this work, we survey the literature on protein cavity computation and classify algorithmic approaches into three categories: evolution‐based, energy‐based and geometry‐based.