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Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey
Author(s) -
Simões Tiago,
Lopes Daniel,
Dias Sérgio,
Fernandes Francisco,
Pereira João,
Jorge Joaquim,
Bajaj Chandrajit,
Gomes Abel
Publication year - 2017
Publication title -
computer graphics forum
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.578
H-Index - 120
eISSN - 1467-8659
pISSN - 0167-7055
DOI - 10.1111/cgf.13158
Subject(s) - molecular graphics , protein data bank , computer science , computer graphics , graphics , grid , centroid , tessellation (computer graphics) , protein data bank (rcsb pdb) , computer graphics (images) , computation , graphics processing unit , geometric modeling , protein crystallization , algorithm , geometric design , surface (topology) , protein structure , geometry , artificial intelligence , mathematics , chemistry , biochemistry , organic chemistry , stereochemistry , crystallization , operating system
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.