CCK-6

The next Comp Chem Kitchen for computational chemists, cheminformaticians, and molecular modelers will be on Thursday January 12th, 2017, at 5.00 pm in the Abbot’s Kitchen in the Inorganic Chemistry Laboratory. Our main speaker will be: Dr Russell Viner from Syngenta, UK, on Structure-Based Design of a Novel Class of Herbicidal HPPD Inhibitors. You can register here.

Refreshments will be provided.

We will also have a lightning talk:
  • Anthony Bradley (Chemistry / DLS)  MMTF: Faster access to protein structure data from the PDB
Please get in touch to volunteer (or nominate) anyone (students, postdocs, professionals, PIs, Emeritus Professors) to give a “lightning talk” of up to 5 minutes. The talks usually resemble one of the following styles:
  • an overview of computational chemistry in your research
  • a (live!) demonstration of some software that you are developing or using
  • a summary of a computational chemistry paper, method, or tool that you’ve seen recently

See previous CCK announcements for examples. Contact Garrett M. Morris, Richard Cooper, Phil Biggin or Rob Paton to volunteer.

CCK-5 [including RDKit workshop]

evotecukCCK-5, on Tuesday, November 1st, 2016, will be another “two-parter” comprised of CCK-5.1 and CCK-5.2. We would like to thank Evotec(UK) Ltd. for supporting this event.

For our fifth meeting, CCK-5.1, on Tuesday, November 1st, 2016, we are honoured to be hosting Greg Landrum; he is the leading developer of the open source cheminformatics toolkit, RDKit.

RDKit is an open source C++ toolkit for cheminformatics with Python, Java and C# wrappers and a number of KNIME cheminformatics nodes. A full overview of its functionality is provided in the documentation.


CCK-5.1

2:00-4:00 pm
Abbot’s Kitchen, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR:

  • Dr Greg Landrum (VP Life Sciences, KNIME.com; and Managing Director,T5 Informatics GmbH) will run a hands-on workshop and hackathon on RDKit. Please bring your laptop (Windows, Mac or Linux): and don’t worry if you do not have RDKit installed. We will help you get set up.

A total of 35 places are available, please register early to avoid disappointment. Registration  for CCK-5.1.


CCK-5.2

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-5.2.

CCK-3

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”.


CCK-3.1

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.


CCK-3.2

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.

Speakers

  • 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.

First meeting

CCK-1 (Tuesday 24th May)

In the spirit of the name, our inaugural meeting, CCK-1 will be held in the Abbott’s Kitchen in the Inorganic Chemistry Laboratory at 5pm on Tuesday May 24th 2016 (5th Week).

Refreshments will be provided.

Jerome Wicker from Chemistry will be speaking about “Machine learning for classification of solid form data extracted from CSD and ZINC”. The software tools discussed include RDKit, CSD, and scikit-learn.

There will also be 2 lightning talks, each ~5 minutes long. Hannah Patel from the Department of Statistics will speak on “Novelty Score: Prioritising compounds that potentially form novel protein-ligand interactions and novel scaffolds using an interaction centric approach”. Software covered will include Django and RDKit. Dr Michael Charlton from InhibOx will also speak on his latest research.