Announcing the “Molecule Combinatorics” and “Chemoinformatics” Discussion Group

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).

  1. Some information on the planned literature can be found at:
  2. An example of an earlier summary lecture can be found at:;
  3. and of a mini-workshop at Slide 6 of the above Lecture;
  4. and of a review (we are still working on the “Molecular Dynamics” review) at:

If you are interested in participating, please email Jotun Hein at hein AT


The fourth Comp Chem Kitchen for computational chemists, cheminformaticians, and molecular modelers will be on Tuesday October 4th, 2016, at 5.30 pm in the ICL Abbot’s Kitchen. Confirmed speaker: Dr Nathan Brown from The Institute of Cancer Research, London, who will speak about his recent paper on the origins of three-dimensionality in drug-like molecules.

Lightning talks (5 minutes or fewer):
Refreshements provided. Five-minute lightning contributions welcome – contact Garrett M. Morris, Richard Cooper, Phil Biggin or Rob Paton.


Our third  meeting, CCK-3, on Tuesday, July 12th, 2016, will be a little different: it will be a two-parter, CCK-3.1 and CCK-3.2:

The Cambridge Crystallographic Data Centre (CCDC) has been hosting and distributing the Cambridge Structural Database (CSD) for 50 years, and its latest release, CSD 2016, is the “world’s essential database of crystal structures, [with] over 800,000 entries”.


1:30-3:30 pm
IT Teaching Laboratory (LG.02) of the Department of Statistics, 24-29 St Giles’, Oxford, OX1 3LB:

Andrew Maloney & Peter Wood (CCDC): CSD Python API Workshop and Hackathon. (We are planning to provide hands-on access to the API, and since  there are only 48 desktops, so you should make sure to book a ticket.)

Register for CCK-3.1.


5.00 – 6:00 pm
Talks and refreshments/beer, will again be held in the Abbot’s Kitchen in the Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR:

Register for CCK-3.2.

If you have a 5-minute Lightning Talk you’d like to give, get in touch!

Also, if you have some code you’d like demo, bring your laptop/mobile device.
Refreshments will be provided, including beer. (Thank you to Prof. Phil Biggin and the MRC Proximity to Discovery Fund for supporting CCK.)

CCK-2 (Tuesday 14th June)

Our second meeting, CCK-2 will be held in the Abbott’s Kitchen in the Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR at 5 pm on Tuesday June 14th 2016 (8th Week). Free tickets are available.


  • Mike Bodkin (Vice President, Research Informatics, Evotec), “Chemical space and how to warp drive discovery”.
  • Jonathan Yates (Department of Materials, University of Oxford), Lightning talk,  “A brief introduction to the Collaborative Computational Project for NMR Crystallography (CCP-NC)”.
  • Jonny Brooks-Bartlett (Elspeth Garman Group, Department of Biochemistry); Lightning talk: “The Julia Programming Language”.
  • Fernanda Duarte (Rob Paton Group, Department of Chemistry, University of Oxford): Lightning talk: “Exploring biochemical systems using the Empirical Valence Bond (EVB) approach”.
  • Matteo Degiacomi (Justin Benesch Group, Department of Chemistry, University of Oxford): Lightning talk: “The Python package BiobOx: a collection of data structures, tools and methods for biomolecular modelling” BiobOx is used for manipulation, measurement, analysis and assembly of atomistic and super coarse-grain structures as well as EM maps.

Talks will take place between 5pm and 6pm, please stay for refreshments and chat afterwards.

We would like to thank Prof. Philip Biggin and the MRC Proximity to Discovery Fund for supporting CCK.