Vasmatzis G, Brower R, Delisi C
Department of Biomedical Engineering, Boston University College of Engineering, Massachusetts 02215.
Biopolymers. 1994 Dec;34(12):1669-80. doi: 10.1002/bip.360341211.
A two-stage method is developed to search the conformational space of small protein segments for low energy structures. Central features of the method are efficient procedures for generating small, eight-backbone atom, local moves in Cartesian coordinates and for introducing geometric constraints in adaptable Monte Carlo procedures. This allows natural implementation of an adaptive simulated annealing algorithm, which achieves an effective trade-off between speed and acceptance ratio. The method is applied to the calculation of various immunoglobulin loops. We also develop data base derived rules for identifying constraint condition, and show that the incorporation of an identified side-chain constraint allows a 1.2 A all-backbone atom rms deviation prediction of a 9 residue long L1 loop.
开发了一种两阶段方法来搜索小蛋白质片段的构象空间以寻找低能量结构。该方法的核心特点是有高效的程序，用于在笛卡尔坐标中生成包含八个主链原子的小局部移动，以及在自适应蒙特卡罗程序中引入几何约束。这使得自适应模拟退火算法能够自然实现，该算法在速度和接受率之间实现了有效的权衡。该方法应用于各种免疫球蛋白环的计算。我们还开发了基于数据库的规则来识别约束条件，并表明纳入识别出的侧链约束可实现对9个残基长的L1环的全主链原子均方根偏差预测，偏差为1.2埃。
