Zhu Fangqiang, Agrafiotis Dimitris K
Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 665 Stockton Drive, Exton, Pennsylvania 19341, USA.
J Comput Chem. 2007 May;28(7):1234-9. doi: 10.1002/jcc.20622.
A novel self-organizing algorithm for conformational sampling is introduced, in which precomputed conformations of rigid fragments are used as templates to enforce the desired geometry. Starting from completely random coordinates, the algorithm repeatedly superimposes the templates to adjust the positions of the atoms, thereby gradually refining the conformation of the molecule. Combined with pair-wise adjustments of the atoms to resolve steric clashes, conformations that satisfy all geometric constraints can be generated from this procedure. The algorithm is demonstrated to achieve good performance and promises potential applications on more challenging modeling problems.
介绍了一种用于构象采样的新型自组织算法，其中预先计算的刚性片段构象用作模板以强制实现所需的几何形状。从完全随机的坐标开始，该算法反复叠加模板以调整原子的位置，从而逐步优化分子的构象。结合原子的成对调整以解决空间冲突，通过此过程可以生成满足所有几何约束的构象。结果表明该算法具有良好的性能，并有望在更具挑战性的建模问题上得到潜在应用。
