Lehtonen J V, Denessiouk K, May A C, Johnson M S
Department of Biochemistry and Pharmacy, Abo Akademi University, Turku, Finland.
Proteins. 1999 Feb 15;34(3):341-55. doi: 10.1002/(sici)1097-0134(19990215)34:3<341::aid-prot7>3.0.co;2-z.
We have developed a generic tool for the automatic identification of regions of local structural similarity in unrelated proteins having different folds, as well as for defining more global similarities that result from homologous protein structures. The computer program GENFIT has evolved from the genetic algorithm-based three-dimensional protein structure comparison program GA_FIT. GENFIT, however, can locate and superimpose regions of local structural homology regardless of their position in a pair of structures, the fold topology, or the chain direction. Furthermore, it is possible to restrict the search to a volume centered about a region of interest (e.g., catalytic site, ligand-binding site) in two protein structures. We present a number of examples to illustrate the function of the program, which is a parallel processing implementation designed for distribution to multiple machines over a local network or to run on a single multiprocessor computer.
我们开发了一种通用工具，用于自动识别具有不同折叠的不相关蛋白质中局部结构相似性的区域，以及定义由同源蛋白质结构产生的更全局的相似性。计算机程序GENFIT是基于遗传算法的三维蛋白质结构比较程序GA_FIT发展而来的。然而，GENFIT可以定位并叠加局部结构同源性区域，而不管它们在一对结构中的位置、折叠拓扑或链方向如何。此外，可以将搜索限制在两个蛋白质结构中以感兴趣区域（例如催化位点、配体结合位点）为中心的体积内。我们给出了一些例子来说明该程序的功能，该程序是一个并行处理实现，设计用于通过本地网络分发到多台机器上，或在单台多处理器计算机上运行。
