Hi Naruki,
Welcome to the list. I wish you all the best - this would be a great
improvement to Open Babel.
Regards,
- Noel
On 25 April 2018 at 12:18, Naruki Yoshikawa <naruki.yoshik...@gmail.com>
wrote:
> Hi everyone,
>
> I am going to work on the project "Fast, Efficient Fragment-Based
> Coordinate Generation"
> https://summerofcode.withgoogle.com/projects/#5029822145757184
> during Google Summer of Code 2018.
> The goal of this project is to implement a fast and efficient method to
> predict 3-D coordinates.
> I'm happy to work with my mentor Geoff Hutchison and the Open Babel
> community.
>
> The first month of GSoC is the Community Bonding period.
> I would like to interact with the Open Babel community.
> Any comments are welcome.
>
>
> Project abstract:
> 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.
>
>
> Thanks,
> Naruki
>
> ---
> Naruki Yoshikawa
> Department of Computational Biology and Medical Sciences,
> Graduate School of Frontier Sciences
> The University of Tokyo
>
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