Hi Naruki,
that's a pretty interesting project, and very interesting for those using
OpenBabel in their projects.
I don't have much experience on inorganic and organometallic molecules, but for
organic molecules I'll be happy to provide examples that are of particular
relevance to biology and drug design.
Good luck with your project,
S
On 04/25/2018 04:18 AM, Naruki Yoshikawa 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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Stefano Forli, PhD
Assistant Professor
Dept. of Integrative Structural
and Computational Biology, MB-112A
The Scripps Research Institute
10550 North Torrey Pines Road
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email: fo...@scripps.edu
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