Computer Physics Communications 181 (2010) 2116–2125 Contents lists available at ScienceDirect Computer Physics Communications www.elsevier.com/locate/cpc CAVE: A package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins ✩ Ján Buša a,b,c , Shura Hayryan a , Chin-Kun Hu a,d,∗ , Jaroslav Skˇ rivánek a,e , Ming-Chya Wu a,f,g a Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan b Technical University in Košice, 040 01 Košice, Slovak Republic c Joint Institute for Nuclear Research, Dubna, Russia d Center for Nonlinear and Complex Systems and Department of Physics, Chung Yuan Christian University, Chungli 32023, Taiwan e SORS Research, 04001 Košice, Slovak Republic f Research Center for Adaptive Data Analysis, National Central University, Chungli 32001, Taiwan g Department of Physics, National Central University, Chungli 32001, Taiwan article info abstract Article history: Received 22 March 2010 Received in revised form 20 August 2010 Accepted 24 August 2010 Available online 17 September 2010 Keywords: Internal cavities Excluded volume Proteins Triangulation Fortran package SMMP ARVO CAVE We developed a software package (CAVE) in Fortran language to detect internal cavities in proteins which can be applied also to an arbitrary system of balls. The volume, the surface area and other quantitative characteristics of the cavities can be calculated. The code is based on the recently suggested enveloping triangulation algorithm [J. Buša et al., J. Comp. Chem. 30 (2009) 346] for computing volume and surface area of the cavity by analytical equations. Different standard sets of atomic radii can be used. The PDB compatible file containing the atomic coordinates must be stored on the disk in advance. Testing of the code on different proteins and artificial ball systems showed efficiency and accuracy of the algorithm. The program is fast. It can handle a system of several thousands of balls in the order of seconds on contemporary PC’s. The code is open source and free. Program summary Program title: CAVE Catalogue identifier: AEHC_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEHC_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 8670 No. of bytes in distributed program, including test data, etc.: 100 131 Distribution format: tar.gz Programming language: Fortran Computer: PC Pentium and Core Operating system: Linux system and Windows XP system Classification: 16.1 Nature of problem: Molecular structure analysis. Solution method: Analytical method for cavities detection, and numerical algorithm for volume and surface area calculation based on the analytical formulas, after using the stereographic transformation. Running time: Depends on the size of the molecule under consideration. The test example included in the distribution takes about 1 minute to run.  2010 Elsevier B.V. All rights reserved. ✩ This paper and its associated computer program are available via the Computer Physics Communications homepage on ScienceDirect (http://www.sciencedirect.com/ science/journal/00104655). * Corresponding author (Chin-Kun Hu) at: Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan. E-mail addresses: Jan.Busa@tuke.sk (J. Buša), shura@phys.sinica.edu.tw (S. Hayryan), huck@phys.sinica.edu.tw (C.-K. Hu), Jaroslav.Skrivanek@tuke.sk (J. Skˇ rivánek), mcwu@ncu.edu.tw (M.-C. Wu). 0010-4655/$ – see front matter  2010 Elsevier B.V. All rights reserved. doi:10.1016/j.cpc.2010.08.032