CCK-7

TL;DR: CCK-7, the 7th of our new series of meetings for computational chemists, cheminformaticians, and molecular modelers, is on Thursday, March 16th, 2017, at 5 pm in the Abbot’s Kitchen, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR. Free tickets are available.

Dear Friends and Colleagues,

Please join us for our next “Comp Chem Kitchen”, CCK-7, at 5-6 pm on Thursday, March 16th, 2017, in the Abbot’s Kitchen, Inorganic Chemistry Laboratory, South Parks Road, Oxford. We are really pleased to announce Prof. Val Gillet, Professor of Cheminformatics at the Information School, University of Sheffield UK, will be speaking:

  • Prof. Val Gillet (Information School, University of Sheffield): “From spectral clustering to spectral geometry: applications in chemoinformatics“. The talk will focus on two distinct but related projects. The first describes the development of spectral clustering for large datasets of up to 100K compounds. One of the main advantages of spectral clustering over more conventional methods is that it permits overlapping clusters, whereby a molecule may belong to more than one cluster. It is also straight-forward to implement clustering with an asymmetric similarity index such as the Tversky index which offers some advantages for the clustering of molecular fragments. We also describe the development of a method for alignment-independent molecular shape comparison based on spectral geometry techniques and present preliminary results for this approach.

Lightning Talks:

  • Max Pillong (Novartis, Basel) “HSM: A novel peptide descriptor and its application to in silico peptide design
  • Dr Anthony Bradley (Project Leader – OxXChem at University of Oxford): “Hands-on: introduction to Git“.
  • Susan Leung (OPIG, University of Oxford): “Hands-on: Using Pandas with RDKit“.

Get in touch if you would like to give a 5 minute talk at a future CCK on your latest research or give a quick demo your latest programming project, or even to nominate someone (students, postdocs, professionals, PIs, Emeritus Professors). 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; or
  • a summary of a computational chemistry paper, method, programming language, or tool that you’ve seen recently.

Refreshments will be provided, including beer.

We would like to thank the University of Oxford MPLS Network and Interdisciplinary Fund for making CCK possible.

About CCK

Comp Chem Kitchen is a regular forum and seminar series to hear about and discuss computational methods for tackling problems in chemistry, biochemistry and drug discovery. It focuses principally on cheminformatics, computational chemistry, and molecular modelling, and overlaps with neighboring areas such as materials properties and bioinformatics.

We’re keen to encourage people involved in coding and methods development (i.e. hackers, in the original untarnished sense of the word) to join us. Our hope is that we will share best practices, even code snippets and software tools, and avoid re-inventing wheels.

In addition to local researchers, we invite speakers from industry and non-profits from time to time, and occasionally organize software demos and tutorials.

If you’re interested in giving a talk, here are some possible topics:

  • Software development (e.g.: Python, C, C++, CUDA, shell, Matlab);
  • Optimizing force field parameters & EVB models;
  • Cheminformatics (e.g.: RDKit);
  • X-ray and NMR crystallography, including small molecule and macromolecular;
  • Protein & RNA modeling, including Molecular Dynamics;
  • Virtual screening and Docking;
  • Machine Learning;
  • Quantum Methods, including DFT.

Bring your laptops, by the way, if you have something you’d like to show!

 

Want to speak? Ideas for speakers?

* If you have ideas for speakers, or would like to give a talk, let us know. We also invite lightning talks of 5 minutes (or fewer) from attendees, so if you have some cool code you’ve been working on and would like to demo, bring your laptop, smartphone, tablet, (wearable?) and tell us all about it. *

Please pass this message on to friends, colleagues, and students who may be interested too!

The main CCK web site is: http://compchemkitchen.org/
Follow us on Twitter: @CompChemKitchen
See you soon! We’re looking forward to seeing and hearing about the diverse range of computational molecular science that you’re cooking up…

—Garrett, Richard, Phil and Rob

garrett.morris@stats.ox.ac.uk
richard.cooper@chem.ox.ac.uk
phil.biggin@bioch.ox.ac.uk
robert.paton@chem.ox.ac.uk

“Mathematical Chemistry and ChemoInformatics”

Announcement forwarded on behalf of Prof. Jotun Hein <hein@stats.ox.ac.uk>, Chair of Bioinformatics, Department of Statistics:

Mathematical Chemistry and ChemoInformatics

Would you like an introduction to mathematical chemistry based on the material from a recent book? Then you may want to come to the talk Monday 7th November 2-4 PM in IT Teaching Room, Department of Statistics.

The talk is given by Jotun Hein and William Kurdahl from the science book discussion club.

The book covers the combinatorics of molecules (especially Polya-Counting), their embedding in 3D Euclidian Space, Chirality, Stereoisomers and a series of application using the program MOLGEN. We are motived to study this book since William is working on models of origin life involving small molecules, but it is obvious that the field could be a rich source of statistical problems to work on.

The slides can be found here:  http://preview.tinyurl.com/MoleculeCombinatorics

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: http://tinyurl.com/http-molecombi-coml
  2. An example of an earlier summary lecture can be found at: http://tinyurl.com/Leimkuhler;
  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: http://preview.tinyurl.com/steel16bookreview.

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

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.)