Starting point to molecular design: Efficient automated 3D model builder key3D

Abstract

Obtaining three-dimensional (3D) structures from structural formulae is a crucial process in molecular design. We have developed a new 3D model builder, Key3D, in which the simplified distance geometry technique and structure optimization based on the MMFF force field are combined. In an evaluation study using 598 crystal structures, the high performance and accuracy of Key3D were demonstrated. In the "flexible-fitting" test, which is focused on practical usefulness in the molecular design process, 88% of the Key3D structures acceptably reproduced the reference crystal structures (root-mean-square deviation <0.6 Å) upon rotation of acyclic bonds. These results indicate that Key3D will be very effective in providing starting points for practical molecular design. © 2006 Pharmaceutical Society of Japan.