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

• Published in: Computer physics communications Vol. 181; no. 12; pp. 2116 - 2125
• Main Authors: Buša, Ján, Hayryan, Shura, Hu, Chin-Kun, Skřivánek, Jaroslav, Wu, Ming-Chya
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01-12-2010
• Subjects: ARVO; CAVE; Excluded volume; Fortran package; Internal cavities; Proteins; SMMP; Triangulation; Proteins; Triangulation; CAVE; Internal cavities; Excluded volume; ARVO; Fortran package; SMMP
• ISSN: 0010-4655; 1879-2944
• DOI: 10.1016/j.cpc.2010.08.032

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 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.