Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey. (1st June 2017)

• Record Type: Journal Article
• Authors: Simões, Tiago; Lopes, Daniel; Dias, Sérgio; Fernandes, Francisco; Pereira, João; Jorge, Joaquim; Bajaj, Chandrajit; Gomes, Abel
• Is Part Of: Computer graphics forum. Volume 36:Number 8(2017)
• Page Start: 643
• Page End: 683
• Publication Date: 2017-06-01
• Subjects: biological modelling -- modelling -- geometric modelling -- computational geometry -- 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; Computer graphics -- Periodicals; 006.605
• DOI: 10.1111/cgf.13158
• Languages: English
• ISSNs: 0167-7055

Abstract

Abstract: 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. Abstract : 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.