Burba Anne E Counterman, Lehnert Ursula, Yu Eric Z, Gerstein Mark
Department of Molecular Biophysics and Biochemistry, Yale University New Haven, CT 06520, USA.
Bioinformatics. 2006 Nov 15;22(22):2735-8. doi: 10.1093/bioinformatics/btl274. Epub 2006 Oct 23.
In many proteins, helix-helix interactions can be critical to establishing protein conformation (folding) and dynamics, as well as determining associations between protein units. However, the determination of a set of rules that guide helix-helix interaction has been elusive. In order to gain further insight into the helix-helix interface, we have developed a comprehensive package of tools for analyzing helix-helix packing in proteins. These tools are available at http://helix.gersteinlab.org. They include quantitative measures of the helix interaction surface area and helix crossing angle, as well as several methods for visualizing the helical interaction. These methods can be used for analysis of individual protein conformations or to gain insight into dynamic changes in helix interactions. For the latter purpose, a direct interface from entries in the Molecular Motions Database to the HIT site has been provided.
在许多蛋白质中，螺旋-螺旋相互作用对于确立蛋白质构象（折叠）和动力学，以及确定蛋白质单元之间的缔合可能至关重要。然而，一套指导螺旋-螺旋相互作用的规则却难以确定。为了更深入地了解螺旋-螺旋界面，我们开发了一套用于分析蛋白质中螺旋-螺旋堆积的综合工具包。这些工具可在http://helix.gersteinlab.org获取。它们包括螺旋相互作用表面积和螺旋交叉角的定量测量，以及几种可视化螺旋相互作用的方法。这些方法可用于分析单个蛋白质构象，或深入了解螺旋相互作用的动态变化。为了实现后一目的，已提供了从分子运动数据库中的条目到HIT站点的直接接口。
