ArticleComputer graphics forum : journal of the European Association for Computer Graphics2017
Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey.
Article in Computer graphics forum : journal of the European Association for Computer Graphics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- pyCAST, a Python package for the detection of cavities on surface proteins.Computational and structural biotechnology journal · 2025Article
- CageCavityCalc (Journal of chemical information and modeling · 2024Article
- CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm.Journal of cheminformatics · 2024Article
- In Silico Exploration of the Trypanothione Reductase (TryR) ofInternational journal of molecular sciences · 2023Article
- SiteFerret: Beyond Simple Pocket Identification in Proteins.Journal of chemical theory and computation · 2023Article
- KVFinder-web: a web-based application for detecting and characterizing biomolecular cavities.Nucleic acids research · 2023Article
- A computational and laboratory approach for the investigation of interactions of peptide conjugated natural terpenes with EpHA2 receptor.Journal of molecular modeling · 2023Article
- xProtCAS: A Toolkit for Extracting Conserved Accessible Surfaces from Protein Structures.Biomolecules · 2023Article
- CAVIAR: a method for automatic cavity detection, description and decomposition into subcavities.Journal of computer-aided molecular design · 2021Article
- Detection of cave pockets in large molecules: Spaces into which internal probes can enter, but external probes from outside cannot.Biophysics and physicobiology · 2019Article
- An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel.Molecules (Basel, Switzerland) · 2018Article
- P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure.Journal of cheminformatics · 2018Article
- ChannelsDB: database of biomacromolecular tunnels and pores.Nucleic acids research · 2018Article
- GPU-based detection of protein cavities using Gaussian surfaces.BMC bioinformatics · 2017Article
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Authors and funding
8 authors.
Funding
Abstract
Detecting and analyzing protein cavities provides significant information about active sites for biological processes (e.g., protein-protein or protein-ligand binding) in molecular graphics and modeling. Using the three-dimensional 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.
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