Higa R H, Oliveira A G, Horita L G, Miura R T, Inoue M K, Kuser P R, Mancini A L, Yamagishi M E B, Togawa R C, Neshich G
Núcleo de Bioinformática, Centro Nacional de Pesquisa Agropecuária, Empresa Brasileira de Pesquisa Agropecuária, Campinas, SP, Brazil.
Bioinformatics. 2004 Aug 12;20(12):1989-91. doi: 10.1093/bioinformatics/bth190. Epub 2004 Mar 25.
Two web-based applications to analyze amino acids three-dimensional (3D) local environment within protein structures-SCORPION and FORMIGA-are presented. SCORPION and FORMIGA produce a graphical presentation for simple statistical data showing the frequency of residue occurrence within a given sphere (defined here as the 3D contacts). The center of that sphere is placed at the Calpha and at the last heavy atom in the side chain of the selected amino acid. Further depth of detail is given in terms of a secondary structure to which the profiled amino acid belongs. Results obtained with those two applications are relevant for estimating the importance of the amino acid 3D local environment for protein folding and stability. Effectively, SCORPION and FORMIGA construct knowledge-based force fields. The difference between SCORPION and FORMIGA is in that the latter operates on protein interfaces, while the former only functions for a single protein chain. Both applications are implemented as stand-alone components of STING Millennium Suite.
http://sms.cbi.cnptia.embrapa.br/SMS, http://trantor.bioc.columbia.edu/SMS, http://mirrors.rcsb.org/SMS, http://www.es.embnet.org/SMS and http://www.ar.embnet.org/SMS. [options: Scorpion, Formiga]
本文介绍了两款基于网络的应用程序——SCORPION和FORMIGA，用于分析蛋白质结构中氨基酸的三维（3D）局部环境。SCORPION和FORMIGA会生成简单统计数据的图形展示，显示给定球体（在此定义为3D接触）内残基出现的频率。该球体的中心位于所选氨基酸侧链的α碳原子和最后一个重原子处。还会根据被分析氨基酸所属的二级结构提供更详细的信息。使用这两款应用程序获得的结果对于评估氨基酸3D局部环境对蛋白质折叠和稳定性的重要性具有参考价值。实际上，SCORPION和FORMIGA构建了基于知识的力场。SCORPION和FORMIGA的不同之处在于，后者作用于蛋白质界面，而前者仅对单个蛋白质链起作用。这两款应用程序均作为STING Millennium Suite的独立组件实现。
