Aksianov Evgeniy, Alexeevski Andrei
Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1-40, Moscow 119991, Russia.
J Bioinform Comput Biol. 2012 Apr;10(2):1241003. doi: 10.1142/S021972001241003X.
The description of a protein fold is a hard problem due to significant variability of main structural units, β-sheets and α-helixes, and their mutual arrangements. An adequate description of the structural units is an important step in objective protein structure classification, which to date is based on expert judgment in a number of cases. Explicit determination and description of structural units is more complicated for β-sheets than for α-helixes due to β-sheets variability both in composition and geometry. We have developed an algorithm that can significantly modify β-sheets detected by commonly used DSSP and Stride algorithms and represent the result as a "β-sheet map," a table describing certain β-sheet features. In our approach, β-sheets (rather than β-strands) are considered as holistic objects. Both hydrogen bonds and geometrical restrains are explored for the determination of β-sheets. The algorithm is implemented in SheeP program. It was tested for prediction architectures of domains from 93 well-defined all-β and α/β SCOP protein domain families, and showed 93% of correct results. The Web-service allows to detect β-sheets in a given protein structure, visualize β-sheet maps, as well as input three-dimensional structures with highlighted β-sheets and their structural features.
由于主要结构单元（β折叠和α螺旋）及其相互排列的显著变异性，蛋白质折叠的描述是一个难题。对结构单元进行充分描述是客观蛋白质结构分类的重要一步，而目前在许多情况下，蛋白质结构分类是基于专家判断的。由于β折叠在组成和几何形状上的变异性，明确确定和描述β折叠的结构单元比α螺旋更为复杂。我们开发了一种算法，该算法可以显著修改常用的DSSP和Stride算法检测到的β折叠，并将结果表示为“β折叠图”，即描述某些β折叠特征的表格。在我们的方法中，β折叠（而非β链）被视为整体对象。在确定β折叠时，我们同时探索了氢键和几何约束。该算法在SheeP程序中实现。我们用它对来自93个定义明确的全β和α/β SCOP蛋白质结构域家族的结构域预测架构进行了测试，结果显示正确率达93%。该网络服务可以在给定的蛋白质结构中检测β折叠，可视化β折叠图，还能输入带有突出显示的β折叠及其结构特征的三维结构。
