“Using GPUs with Molecular Dynamics codes: optimizing usage from a user perspective” by Dr. Ole Juul Andersen, Department of Biochemistry, University of Oxford (given at CCK-11, on February 1, 2018).

Slides kindly provided by our CCK speakers.

“Using GPUs with Molecular Dynamics codes: optimizing usage from a user perspective” by Dr. Ole Juul Andersen, Department of Biochemistry, University of Oxford (given at CCK-11, on February 1, 2018).

We all had a lot of fun at our first CCK Hackathon, and our groups explored some very cool ideas using Python, RDKit, the CSD Python API, and CCDC tools such as IsoStar and SuperStar during the day. We came together afterwards, to hear Andrew Moloney from CCDC talk about *“Can we design drugs like we design airplanes? – The ADDoPT Project and the CCDC”*, and to see the fruits of our labors with a series of Lightning Talks summarizing each group’s work. The winners and runners-up received delicious prizes: boxes of chocolates.

Prof. Paul Finn has kindly shared his slides from CCK-9:

Greg Landrum’s RDKit workshop today at CCK-5.1 was excellent: some of the Jupyter notebooks he demoed or used as slides are already available:

https://github.com/rdkit/UGM_2016/tree/master/Notebooks

There are tutorials too.

Enjoy!

Our CCK members might be interested to know Prof. Jotun Hein, Chair of Bioinformatics in the Department of Statistics at the University of Oxford, and his colleagues have decided to spend Michaelmas Term, 2016, on the topics of “Molecule Combinatorics” and “Chemoinformatics”. We will try to focus on the computational and combinatorial aspects of these topics.

We meet at 9 am on Mondays, Wednesdays, and Fridays for 90 minutes in the Department of Statistics, and typically spend about 2 hours preparing. It will probably take about 10 hours per week to participate. We plan to send a review of the first book we will be reading, “Mathematical Chemistry and Chemoinformatics” (2013), to SIAM Review, who have already indicated they are eager to publish it. Jotun also plans to give a 90 minute summary lecture around December 1st, and will also arrange a 4-5 day mini-workshop on the topic at the end of term (possibly November 28th).

- Some information on the planned literature can be found at: http://tinyurl.com/http-molecombi-coml
- An example of an earlier summary lecture can be found at: http://tinyurl.com/Leimkuhler;
- and of a mini-workshop at Slide 6 of the above Lecture;
- and of a review (we are still working on the “Molecular Dynamics” review) at: http://preview.tinyurl.com/steel16bookreview.

If you are interested in participating, please email Jotun Hein at hein AT stats.ox.ac.uk

Here are the slides from Fernanda Duarte’s talk *“Using Valence Bond Theory to Model **(Bio)Chemical Reactivity”* at CCK-2.

Here are the slides from Jerome Wicker, Department of Chemistry, that were presented at CCK-1:

Here are the slides from Michael Charlton, InhibOx, that were presented at CCK-1: