Name
Title | ||
|---|---|---|
Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey. |
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. |
Year | DOI | Venue |
|---|---|---|
2017 | 10.1111/cgf.13158 | COMPUTER GRAPHICS FORUM |
Keywords | Field | DocType |
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 science,Local feature size,Molecular graphics,Computational geometry,Algorithm,Theoretical computer science,Computational science,Geometric design,Tessellation,Graphics processing unit,Protein Data Bank,Grid | Journal |
Volume | Issue | ISSN |
36.0 | 8.0 | 0167-7055 |
Citations | PageRank | References |
2 | 0.36 | 70 |
Authors | ||
8 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Tiago Simões | 1 | 2 | 0.36 |
| Daniel S. Lopes | 2 | 32 | 7.16 |
| Sérgio Dias | 3 | 17 | 2.00 |
| Francisco Fernandes | 4 | 48 | 3.39 |
| João Pereira | 5 | 3 | 0.74 |
| Joaquim A. Jorge | 6 | 1008 | 81.51 |
| Chandrajit L. Bajaj | 7 | 2880 | 306.59 |
| Abel J. P. Gomes | 8 | 82 | 18.04 |