Category Archives: Drug Discovery

CCK-19: Oxford + Cambridge + Berlin

Posted on by

Wednesday, 30 November 2022, 3:30-5 pm GMT

We are delighted to be returning with CCK-19 in the new seminar room of the Dorothy Crowfoot Hodgkin Building (a.k.a. the Phase II Biochemistry Department on Sherrington Road in the heart of the Science Area). We will be meeting jointly with our friends in Cambridge and Berlin via Zoom. We will have talks from Roger Sayle in Cambridge via Zoom, Matteo Ferla in Oxford, and Andrea Volkamer in Berlin, starting at 3:30 pm UK time. After the talks, ~5:15 pm, we will head over to The Royal Oak on Woodstock Road. More details below, and register to attend in person on Eventbrite or register for Zoom here: https://zoom.us/meeting/register/tJApf-uhrD0vH9S1U-9p6il24hB5RHtEh1ii.

Programme

Why Is It So Hard to Search Ultra-Large Chemical Libraries?

Roger Sayle, NextMove Software, Cambridge
https://www.nextmovesoftware.com/people.html

Fragmenstein: Stitching Compounds Together Like a Reanimated Corpse

Matteo Ferla, Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford
https://www.matteoferla.com/

Data-Driven Methods for Active Compound Design and Risk Assessment

Andrea Volkamer, Charité Berlin and Saarland University, Berlin
https://volkamerlab.org/

Locations

Please turn up 10 minutes before the start time to register where needed:

Oxford: Phase II Biochemistry Seminar Room, New Biochemistry Building off South Parks Road

Cambridge: Cambridge Crystallographic Data Centre, Union Road

Berlin: Lecture Hall 1 (1st Floor), Institut für Pharmazie, Königin-Luisestrasse 2+4

After-event Locations

~5:15 pm GMT onwards:

Oxford: The Royal Oak, Woodstock Road

Cambridge: The Alma, Russell Court

Berlin: Luise Dahlem, Königin-Luise-Straße

Please join us in person—just turn up at the Phase II Biochemistry Seminar Room in the Dorothy Crowfoot Hodgkin Building 10 minutes before the start time—or to join remotely please register here:

Register for Zoom: https://zoom.us/meeting/register/tJApf-uhrD0vH9S1U-9p6il24hB5RHtEh1ii

If you would like to present at a future meeting please just let us know (morris [] stats.ox.ac.uk). 🙂

In Person (Oxford, Cambridge or Berlin) & Virtual (Zoom) – Free & open to all
http://www.C-INF.net – https://CompChemKitchen.org/ – http://www.DigiDrug.NET

CCK-18

Posted on by

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.

CCK-16

Posted on by

TL;DR: CCK-16, the next in our series of meetings for computational chemists, cheminformaticians, and molecular modelers, will be on Thursday, October 31st, 2019, at 5:00 pm in the Seminar Room, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU. Free CCK-16 tickets are available.

Dear Friends and Colleagues,

Please join us for our next “Comp Chem Kitchen”, CCK-16, at 5-6 pm on Thursday, October 31st, 2019, in the Seminar Room, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU. We are very pleased to announce Dr Paulo Tosco from Cresset, UK, will be speaking:

Dr Paulo Tosco

Dr Paulo Tosco (Cresset, UK): “Design in 2D, Model in 3D: Live 3D Pose Generation from 2D Sketches”

How nice would it be to be able to draw a molecule in your favourite 2D sketcher, and see in real time how its 3D electrostatic potential looks like, what interactions it makes in the active site, how its shape and electrostatics compare to a known active? This is why we decided to build from ground up a new molecular design platform around this engaging idea. As we started fleshing out the details of the Grow3D algorithm, a number of obvious and more subtle gotchas emerged.

In this talk I will illustrate how we addressed these challenges, and I will also give an overview of the integration of Grow3D in the context of our web-based molecular design platform, showing its effectiveness in bridging the gap between 2D and 3D methods.

Dr Paolo Tosco joined Cresset in 2014 after being an Assistant Professor at the University of Turin, Italy. A medicinal chemist by background, after completing his PhD in Drug Chemistry his main focus became computational chemistry, with a particular interest in development and implementation of novel methods and algorithms. He has been a contributor to many open source projects, most notably the RDKit. His current role at Cresset involves scientific development of the company codebase and technical customer support.

Lightning Talks

  • Mihaela Smilova (SGC):  “Fragment Hotspot Maps to Drive the Elaboration of Fragment Screening Hits“; and
  • Dr Tomasz Piskorz (Department of Chemistry): “A Short Intro to MDAnalysis (A Python Tool to Analyze the Results of MD simulations)”.

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.

Continue reading →

CCK-11

Posted on by

TL;DR: CCK-11, the 11th of our series of meetings for computational chemists, cheminformaticians, and molecular modelers, is on Thursday, February 1st, 2018, at 5 pm in the Seminar Room, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU. Free CCK-11 tickets are available.

 

Dear Friends and Colleagues,

Please join us for our next “Comp Chem Kitchen”, CCK-11, at 5-6 pm on Thursday, February 1st, 2018, in the Seminar Room, Department of Biochemistry, South Parks Road, Oxford. We are  very pleased to announce Dr Georgia McGaughey, Senior Director, Modeling & Informatics, from Vertex Pharmaceuticals, Boston, USA, will be speaking:

  • Dr Georgia McGaughey (Vertex Pharmaceuticals, Boston, USA): “Shaping Belsomra: Application of Experimental and Theoretical Methods for Driving Synthetic Designs“.
  • Dr Ole Juul Andersen (Carlsberg Fellow, SBCB, Department of Biochemistry, University of Oxford): “Using GPUs with Molecular Dynamics codes: optimizing usage from a user perspective“.

Lightning Talks

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

[email protected]
[email protected]
philip.biggin@bioch.ox.ac.uk
[email protected]

CCK-9

Posted on by

TL;DR: CCK-9, the 9th of our new series of meetings for computational chemists, cheminformaticians, and molecular modelers, is on Thursday, November 9th, 2017, at 5 pm in the Seminar Room, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU. Free tickets are available.

 

Dear Friends and Colleagues,

Please join us for our next “Comp Chem Kitchen”, CCK-9, at 5-6 pm on Thursday, November 9th, 2017, in the Seminar Room, Department of Biochemistry, South Parks Road, Oxford. We are very pleased to announce Prof. Paul W. Finn from Oxford Drug Design and the University of Buckingham, will be speaking:

Lightning Talks:

  • Foluso Olungana (Computer Science): “Blockchain and Ethereum“.

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

[email protected]
[email protected]
philip.biggin@bioch.ox.ac.uk
[email protected]

CCK-4

Posted on by

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.