Chemical information is provided in various formats. Open Babel is a tool to convert file formats. When we translate a format which does not include 3-D coordinate information into a format which requires it, we must predict coordinates. Open Babel implements a rule-based coordinate prediction method, but the current implementation is problematic. It sometimes fails when we treat inorganic and organometallic molecules, and by relying on force field geometry optimization, it is slower than distance-geometry or fragment-based methods.

This is a proposal to implement a fast and efficient method to calculate 3-D coordinates using fragment information. Since fragments can decide the position of many atoms at once and minimize the need for conformer sampling, this approach is more efficient. P. Baldi's paper in 2013 reports that their fragment-based method is more accurate and 10 times faster than Open Babel. Implementing a better prediction method is beneficial for chemistry and leads to new discoveries in the field of drug design.

Organization

Student

Naruki Yoshikawa

Mentors

  • Geoff Hutchison
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2018