CAVE swMATH ID: 9282 Software Authors: Buša, Ján; Hayryan, Shura; Hu, Chin-Kun; Skřivánek, Jaroslav; Wu, Ming-Chya Description: CAVE: A package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins. 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, 346 ff (2009)] 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. Homepage: http://www.sciencedirect.com/science/article/pii/S0010465510003395 Keywords: excluded volume; triangulation; Fortran package; SMMP; ARVO Related Software: SURFNET; VADAR; SMMP; ARVO; CMPGRD; SimWall; HEDP; Chromium; ParaView; CAVE-CL; OpenCL Cited in: 3 Publications all top 5 Cited by 10 Authors 2 Buša, Ján 2 Hayryan, Shura A. 2 Hu, Chinkun 2 Wu, Ming-Chya 1 Buša, Ján jun. 1 Chen, Jianjun 1 Skřivánek, Jaroslav 1 Xie, Lijun 1 Zheng, Yao 1 Zou, Jianfeng Cited in 2 Serials 2 Computer Physics Communications 1 Communications in Computational Physics Cited in 2 Fields 2 Biology and other natural sciences (92-XX) 1 Fluid mechanics (76-XX) Citations by Year