Category Archives: RDKit

CCK-20: Greg Landrum – Monday 20 November 17:00 GMT, Stats + Zoom

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TL;DR: CCK-20: Greg Landrum — the next in our series of meetings for computational chemists, cheminformaticians, and molecular modelers, is on Monday November 20th, 2023, at 5:00 pm GMT in person in the Large Lecture Theatre of the Department of Statistics, 24-29 St Giles’, Oxford, OX1 3LB. Refreshments at 4:30 pm. Attendance is free, and open to all. Register for Zoom (100 online attendees max).

Dear Friends and Colleagues,

The next Comp Chem Kitchen, CCK-20, is on Monday, November 20th, 2023, at 5-6 pm GMT. We’re delighted to announce Dr Greg Landrum from ETH Zürich will be speaking. We will be in the Large Lecture Theatre on the Lower Ground floor of the Department of Statistics, 24-29 St Giles’. Join us early for refreshments—including beer—from ~4:30 pm, in the Ground Floor Social Area in Stats. Attendance is free and open to all.

We will also be broadcasting on Zoom, but you must register for Zoom first—and there are only 100 spaces on Zoom.

5 pm: Dr Greg Landrum: “Please stop combining data from different IC50 assays”.

Dr Greg Landrum

Greg is the lead developer of the widely-used open source cheminformatics API, RDKit. Greg is a Senior Scientist at ETH Zürich, Switzerland; and Founder and Managing Director of T5 Informatics GmbH. Greg has been a Senior Advisor to KNIME since 2019. Greg was a Principal Investigator at the Konstanz Research School for Chemical Biology from 2014-2020; and Global Head of Chemical Information Systems for Novartis (2011-2016).

Partially supported by CECAM:

CCK-10 Hackathon

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TL;DR: CCK-10 Hackathon, Part 1 of the 10th in our series of meetings for computational chemists, cheminformaticians, and molecular modelers, is on Wednesday, December 6th, 2017, at 10:30 am – 5 pm in the Computer Suite, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU. We will be learning about the CSD (Cambridge Structural Database) Python API. Bring your own ideas and programming problems. Pizza provided. Part 2, CCK-10,  will take place after the hackathon. Tickets are limited; please book by November 29th, 2017.

 

Dear Friends and Colleagues,

Please join us for our next “Comp Chem Kitchen” CCK-10 Hackathon, at 10:30 am – 5 pm on Wednesday, December 6th, 2017, in the Computer Suite, Department of Biochemistry, South Parks Road, Oxford. We are  pleased to announce that Andrew Maloney from Cambridge Crystallographic Data Centre will be leading the CSD Python API Hackathon.

Please register in advance, by November 29th, 2017, as spaces are limited.

The hackathon will follow this format:

  • 10.30 am: Introduction. CSD Python API overview
    • Quick survey of areas of interest and experience.
    • Assemble 4-8 teams with some expertise in each.
  • 11.00 am – 12.30 pm: Hacking – design and tools
  • 12.30 – 1.00 pm: Five min updates / requests for input
  • 1.00 – 2.00 pm: Lunch
  • 2.00 – 5.00 pm: Hacking
  • 5.00 – 6.00 pm: CCK-10, including Lightning summaries of hacked projects. Tickets are free.

Themes

  • Clustering and visualisation of data points in protein-ligand interaction space.
  • Using PDB data and some protein-ligand interaction descriptors or fingerprints, what can we learn by visualising using PCA or t-SNE clustering?
  • Molecular interaction descriptor space.
  • Using CSD data (and the CSD Python API) can we visualise interaction patterns using simple descriptors of important intermolecular interactions in the solid state. Do these patterns correspond to standard descriptions of molecular packing?

Examples

  • PLIF fingerprints
  • Chem-17 chemical space visualisation
  • dSNAP style interaction scatter plots
  • Interactions as sound
  • Ligplot interaction diagrams
  • Fragment Mapping
  • Constrained conformer generation
  • Hotspot mapping in protein binding sites using IsoStar & SuperStar-like analyses

Pizza and refreshments will be provided.

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.

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-7

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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

[email protected]
[email protected]
[email protected]
[email protected]

CCK-5.1 Quick Poll

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If you’re one of the lucky people who have signed up for the CCK-5.1 workshop and hackathon tomorrow, we’d like to know if you have any special interests, so here’s a link to our quick (3-question) poll:

https://goo.gl/forms/5CuYs96a3XT7Ofrp1

Please bring a laptop to the workshop. If you don’t have an install of RDKit already, we will be installing using conda, according to these instructions: https://github.com/rdkit/conda-rdkit

See you tomorrow!

—The Organizers of Comp Chem Kitchen

CCK-5 [including RDKit workshop]

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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.

First meeting

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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.