UPDATE: We are going virtual! Our next Comp Chem Kitchen, CCK-18, will be a webinar, on Friday, March 27, 2020, at 5-6 pm. We are delighted to announce that Prof. Andreas Bender from the University of Cambridge will be speaking, as well as Dr Vicky Hellon from F1000 Research. To join the webinar, you must sign up for a free ticket (limit 100). Sold out (as of March 23)! We are looking into streaming the event via YouTube. More info soon.

Prof. Andreas Bender

Dr. Andreas Bender (University of Cambridge): “AI in Drug Discovery – What is Realistic, What are Illusions?”

While ‘AI in Drug Discovery’ is currently a hot topic, it is important to be optimistic, yet realistic, about its opportunities in the area: Drugs work in biological systems, which are noisy by their very nature, and which we don’t understand properly. This presentation will outline approaches and applications of AI in the drug discovery field, with a particular focus on data currently available to us, and challenges with the translation of computational predictions into the physiological (in vivo) context.

Dr Andreas Bender is a Reader for Molecular Informatics with the Centre for Molecular Science Informatics at the Department of Chemistry of the University of Cambridge, leading a group of about 15 postdocs, PhD and graduate students and academic visitors in the area of life science data analysis. In parallel, he leads a team in Computational Drug Safety and ADME within the Clinical Pharmacology & Safety Sciences group at AstraZeneca in Cambridge (CPSS DSAI). In his work, Andreas is involved with the integration and analysis of chemical and biological data, aimed at understanding phenotypic compound action (such as cellular readouts, and also organism-level effects) on a mechanistic level, predicting molecular properties related to both compound effiacy and toxicity, as well as drug repurposing. He received his PhD from the University of Cambridge and worked in the Lead Discovery Informatics group at Novartis in Cambridge, MA, USA, as well as at Leiden University in the Netherlands before his current post. In 2013 he was awarded an ERC Starting Grant to model mixture effects of chemical structures in biological systems using mechanistic approaches, an area currently very little understood.

Dr Bender is a Reader for Molecular Informatics, at the Centre for Molecular Informatics in the Department of Chemistry, University of Cambridge; and Associate Director of Computational ADME/Tox (CPSS-DSAI), at AstraZeneca, Cambridge, UK,

Vicky Hellon (Associate Publisher, F1000Research): “F1000Research: Open Access publishing and Chemoinformatics

F1000 Research was established as a publishing platform in 2013 with the aim of pioneering open research through open data, open peer review and transparency throughout the publication process. The talk will discuss open publishing in general, how the publication model at F1000Research works and how this differs from more ‘traditional’ scientific publishing. There will also be discussion on the F1000Research Chemical Information Science Gateway and our experiences of publishing in the Chemoinformatics/software area.

Vicky Hellon is the Associate Publisher at F1000Research which she joined in 2017 after previous roles in Open Access publishing at Nature Research. Her role encompasses developing content across F1000Research, building collaborations and supporting the development of funder specific publishing platforms, particularly Wellcome Open Research and also HRB Open Research which she is currently project lead on. She is passionate about the progression of open research and particularly enjoys opportunities to actively engage with the research community.

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


TL;DR: CCK-15, the next in our series of meetings for computational chemists, cheminformaticians, and molecular modelers, will be on Thursday, September 5th, 2019, at 5:30 pm in the Large Lecture Theatre LG.01, Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford OX1 3LB. Free CCK-15 tickets are available.

Dear Friends and Colleagues,

Please join us for our next “Comp Chem Kitchen”, CCK-15, at 5:30-6:30 pm on Thursday, September 5th, 2019, in the Large Lecture Theatre LG.01 in the Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford. We are  very pleased to announce Prof. Adrian E. Roitberg from the Department of Chemistry, University of Florida, USA, will be speaking:

  • Prof. Adrian E. Roitberg (Department of Chemistry, University of Florida. Gainesville, FL. 32611-7200, USA; [email protected]):Is Quantum Chemistry Amenable for Machine Learning? Are the Computers Coming for Our Jobs?
    • For decades, computational chemists have been searching for new ways to develop faster and more accurate empirical potentials for application in a myriad of problems. These applications include the calculation of thermochemical properties and theoretical IR spectra, stability comparisons, structural optimization, and molecular dynamics or Monte Carlo simulation. The reason empirical potentials have been so attractive to the community abroad is the promise of accuracy and speed, especially compared to more traditional quantum mechanical or classical methods for computing molecular energies and forces. However, empirical potentials developed using traditional methods have remained at arm’s length for various reasons. Within the last decade, Machine Learning (ML) methods have proved applicable to the development of empirical potentials, specifically methods from deep learning. The ANAKIN-ME (ANI) method, which focuses on the use of large and diverse data sets in training new potentials, has consistently proven to be universally applicable to systems containing the atomic species in the training set. Focusing on parametrization for organic molecules, we have developed a universal ANI potential which is highly accurate compared to reference QM calculations at speeds 107 faster. The ANI potential is shown to accurately represent the underlying physics of molecules through various test cases including: thermochemistry, structural optimization, and molecular dynamics simulations. The results presented here provide evidence of the universal applicability of ANI deep learned potentials to various computational chemistry problems involving organic molecules.

Prof. Roitberg was born and raised in Argentina, and he received his BS degree in Chemistry from the University of Buenos Aires. He then moved to the US to pursue his PhD in chemistry, at the University of Illinois at Chicago, followed by a postdoctoral stay at Northwestern University. He joined a National laboratory (NIST) as staff and moved to the University of Florida as Assistant Professor in 2001. He is now a Full Professor there at UF, in both the Chemistry and Physics Departments. Prof. Roitberg has graduated 20 PhD students so far. He has received several awards, including being named a Fellow of both the American Physical Society and the American Chemical Society. He was also named an Ulam Scholar at Los Alamos National Laboratory and received the Raices Prize (roots) from the Ministry of Science in his native Argentina. Prof. Roitberg has published over 160 scientific articles, and his h-index is 55, with over 24000 citations of his papers.

Lightning Talks

  • Harry Morgan (Physical and Theoretical Chemistry Laboratory. South Parks Road, Oxford, OX1 3QZ, UK): Pressure-induced transitions in vanadium oxyhydrides“.
  • Dr Anthony Nash, PhD, MRSC (Senior Research Scientist, Nuffield Department of Clinical Neurosciences, University of Oxford): Human Centric Drug Discovery Using a Real World Dataset and iPSC-based Assays”.

Refreshments will be provided, including beer.

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

Want to speak? Ideas for speakers?

If you have ideas for speakers, or would like to give a talk, get in touch. 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 it, bring your laptop, smartphone, tablet, (wearable?) and tell us all about it.

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.

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

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!

The main CCK web site is:
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 Fernanda

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