CAVE: A package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins

DOI10.1016/J.CPC.2010.08.032MaRDI QIDQ546795zbMATH OpenOpenAlexWikidataFDO

Authors Ján Buša, Shura Hayryan, Chin-Kun Hu, Jaroslav Skřivánek, Ming-Chya Wu

Publication date 30 June 2011

Published in Computer Physics Communications (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.cpc.2010.08.032

zbMATH Keywords

triangulationexcluded volumeARVOFortran packageSMMP

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Software, source code, etc. for problems pertaining to biology (92-04) Biophysics (92C05)

Recommendations

• CAVE-CL: an OpenCL version of the package for detection and quantitative analysis of internal cavities in a system of overlapping balls: application to proteins
• Detecting cavities in a system of overlapping spheres using enveloping triangulation
• ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations
• A computer method for estimating volumes and surface areas of complex structures consisting of overlapping spheres
• On the definition and the construction of pockets in macromolecules

Cites work

• ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations
• An enhanced version of SMMP-open-source software package for simulation of proteins
• Triangulating the surface of a molecule
• [SMMP] A modern package for simulation of proteins

Cited in

(2)

• CAVE-CL: an OpenCL version of the package for detection and quantitative analysis of internal cavities in a system of overlapping balls: application to proteins
• Detecting cavities in a system of overlapping spheres using enveloping triangulation

Describes a project that uses

Uses Software

• SURFNET
• VADAR
• CAVE
• SMMP
• ARVO

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