Self-organizing superimposition algorithm for conformational sampling.
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.
Zhu
Fangqiang
F
Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 665 Stockton Drive, Exton, Pennsylvania 19341, USA. fzhu2@prdus.jnj.com
Agrafiotis
Dimitris K
DK
D000465:Algorithms; D008958:Models, Molecular; D008968:Molecular Conformation