Gelfand I, Kister A, Kulikowski C, Stoyanov O
Department of Mathematics, Rutgers University, New Brunswick, NJ 08903, USA.
J Comput Biol. 1998 Fall;5(3):467-77. doi: 10.1089/cmb.1998.5.467.
We introduce a new algorithmic method for identifying the geometrical core of proteins that does not require the usual superposition of structures. A geometrical core is defined as the set of residues such that the C alpha (I) - C alpha (J) atom distances are identical in all structures of the protein family under study, where I and J are secondary structure positions in the structural units--strands, loops, or parts of them. The result of applying the algorithm to 53 Ig structures leads to the identification of two geometrical core sets of C alpha atom positions for the VL and VH domains. Applications of the core sets are described.
我们引入了一种新的算法方法来识别蛋白质的几何核心，该方法不需要通常的结构叠加。几何核心被定义为这样一组残基，即在所研究的蛋白质家族的所有结构中，Cα（I）-Cα（J）原子距离是相同的，其中I和J是结构单元（链、环或它们的部分）中的二级结构位置。将该算法应用于53个免疫球蛋白（Ig）结构的结果，导致识别出VL和VH结构域的两个Cα原子位置的几何核心集。描述了核心集的应用。
