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首页> 外文期刊>Computer physics communications >CAVE: A package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins
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CAVE: A package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins

机译:CAVE:用于检测和定量分析重叠球系统中的内腔的软件包:应用于蛋白质

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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. Bu?a 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.
机译:我们用Fortran语言开发了一个软件包(CAVE),以检测蛋白质中的内部空腔,该空腔也可以应用于任意球系统。可以计算空腔的体积,表面积和其他定量特征。该代码基于最近建议的包络三角剖分算法[J. Bu?a et al。,J. Comp。化学30(2009)346]通过解析方程计算腔的体积和表面积。可以使用不同标准的原子半径集。包含原子坐标的PDB兼容文件必须预先存储在磁盘上。对不同蛋白质和人造球系统上的代码进行测试显示了该算法的效率和准确性。该程序速度很快。它可以在当代PC上以秒为单位处理数千个球的系统。该代码是开源和免费的。

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