CCK-11

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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]

Job: XChem Software Engineer, Diamond Light Source

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(From: Frank von Delft, DLS & SGC):

We are recruiting a software engineer (or scientific programmer, or geek-minded scientist, or scientifically-minded geek) to help us get a lot better at designing compounds from hits from crystallographic fragment screening.

The post is linked to the XChem facility at Diamond’s beamline I04-1, set up in partnership with the SGC-Oxford, which is now routinely hosting users every week, allowing them to find convincing fragment hits with a few days’ worth of experiments. In 2017, over 30 users measured over 35,000 crystals in academic and industrial XChem experiments.

To confront the next bottleneck, namely converting low potency fragments into high-potency compounds, we are setting up a suite of easily accessible computational tools that streamline the obvious yet surprisingly fiddly analyses by which to identify the most sensible follow-up compounds that are easy to make or procure.

The (initially) two-year post will, in a team of three and depending on interests, build infrastructure, harden existing algorithms or help evolve new ones, do web interface design, or any combination of the above.

The project is seeding a nascent effort, for now aspirationally code-named CCP-CMC (CompMedChem, http://www.ccp-cmc.org/), to bring the awesome collaborative ethos of CCP4 and other MX tools to computational medicinal chemistry.

Recruitment details are here: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.display_form?p_company=10&p_internal_external=E&p_display_in_irish=N&p_process_type=&p_applicant_no=&p_form_profile_detail=&p_display_apply_ind=Y&p_refresh_search=Y&p_recruitment_id=132678

Deadline is Monday, 29 January, 2018 (it’s wrong in the link).

—
Prof Frank von Delft

[email protected]

Principal Beamline Scientist: I04-1
Diamond Light Source
+44 1235 778997 (office: M,T,T)
+44 7471 026103 (mobile)

Principal Investigator: Protein Crystallography
Structural Genomics Consortium
Oxford University
+44 1865 617583 (office: W,F)

CCK-10 Hackathon Photos

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We all had a lot of fun at our first CCK Hackathon, and our groups explored some very cool ideas using Python, RDKit, the CSD Python API, and CCDC tools such as IsoStar and SuperStar during the day. We came together afterwards, to hear Andrew Moloney from CCDC talk about “Can we design drugs like we design airplanes? – The ADDoPT Project and the CCDC”, and to see the fruits of our labors with a series of Lightning Talks summarizing each group’s work. The winners and runners-up received delicious prizes: boxes of chocolates.

Demonstrating “bindbook”: a kind of Facebook for proteins, and the ligands they ‘like’.

Demonstrating sonification of protein-ligand interactions derived using Blundell et al.’s Arpeggio.

SABS alumnus Saulo Pires de Oliveira receives the prize for the winners of the CCK-10 Hackathon, for their work on evolutionary relationships of binding sites.

Richard Cooper awards the runner-up prize to SABS First Year, Dominik Schwartz, for his group’s sonified protein-ligand interactions project.

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-9

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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-8

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TL;DR: CCK-8, the 8th of our new series of meetings for computational chemists, cheminformaticians, and molecular modelers, is on Thursday, October 26th, 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-8, at 5-6 pm on Thursday, October 26th, 2017, in the Seminar Room, Department of Biochemistry, South Parks Road, Oxford. We are really pleased to announce Prof. Alpha Lee from the Department of Physics, University of Cambridge, UK, will be speaking:

  • Prof. Alpha Lee (Cambridge): Exploring chemical space using random matrix theoryDeveloping computational methods to explore chemical space is a major challenge for drug discovery. The challenge is often the limited number of experimental measurements relative to the vast chemical space. I will discuss a mathematical framework, inspired by random matrix theory, which allows us to remove noise due to finite sampling and identify important chemical features. I will illustrate this framework with three examples: predicting protein-ligand affinity [1], optimal design of experiments by combining coarse and fine measurements [2], and inferring a generative model in chemical space by combining Ornstein-Zernike theory with deep learning [3].[1] A. A. Lee, M. P. Brenner and L. J. Colwell, Proc. Natl. Acad. Sci. U.S.A., 113, 13564 (2016);
    [2] A. A. Lee, M. P. Brenner and L. J. Colwell, Phys. Rev. Lett., accepted (2017) arXiv:1702.06001 [PDF];
    [3] A. A. Lee, arXiv:1706.08466 (2017) [PDF].

Lightning Talks:

  • Simon Nadal (Groups of Prof. Ben Davis, CRL; and Prof. Shabaz Mohammed, Biochemistry): “SILCS simulations in preclinical drug discovery“.
  • Anthony Aimon (Visiting Scientist, OxXChem, i04-1 Beamline, Diamond Light Source): “Opentrons: Automated Organic Synthesis made easy“.

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]

Forthcoming CCK schedule

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Meetings this term

CCK-8 Thursday 26th October (3rd week) 5-6pm Biochemistry Seminar Room

CCK-9 Thursday 9th November (5th week) 5-6pm Biochemistry Seminar Room

CSD / data visualisation hackathon & CCK-10 Wednesday 6th December (9th week) Biochemistry Computer Suite and Seminar Room

All welcome. Beer and refreshments provided. Please register in advance to help keep our catering projections accurate.

Request and suggestions for speakers

Suggestions for speakers are always welcome. Five-minute talks on any CCK related topic are welcome. These range from introductions to your research, and requests for help and collaborations, to expounding the virtues of your favourite programming environment, or a quick analysis of a recent comp chem paper.

Drop us a line if you wish to get involved or make any suggestions.

 

Phil Biggin (Biochem) [email protected]

Richard Cooper (Chem) [email protected]

Garrett Morris (Stats / SABS) [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]