CCK-13 & MGMS: Molecular VR

Please join us for our next “Comp Chem Kitchen”, CCK-13, being jointly held with the Molecular Graphics and Modelling Society:

We are  very pleased to announce Dr David Glowacki from the University of Bristol will be talking and giving live demonstrations of his molecular virtual reality system. He will also be presented with his MGMS Silver Jubilee Award. David’s work has been featured in The New York Times: “It’s Time for a Chemistry Lesson. Put on Your Virtual Reality Goggles.”

If you’re curious and would like to try out molecular VR, please come along!

David R. Glowacki: Carrying out nano-molecular surgery in virtual reality

  • School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
  • Department of Computer Science, University of Bristol, BS8 1UB, UK
  • Pervasive Media Studio, Watershed, 1 Canons Rd, Bristol BS1 5TX, UK
  • [email protected]

Over the past several years, we have been developing a framework for interactive molecular dynamics in a multiuser virtual reality (VR) environment, which combines rigorous cloud-mounted atomistic physics simulations with commodity VR hardware. [1] It allows users to visualize and manipulate, with surgical precision, the structures of complex molecular structures whose dynamics are simulated in real-time onenterprise cloud architectures. [2] It also enables multiple users to inhabit the same virtual environment, facilitating new classes of digital interaction between those users – e.g.,enabling them to pass rigorously simulated virtual objects between one another. This represents a qualitatively new kind of virtual experience beyond what is presently possible even within the large-scale immersive stereoscopic CAVE environments. We have recently completed a series of controlled user studies to evaluate the benefit that this VR framework provides in accelerating research tasks which require sophisticated 3d spatial reasoning (threading methane through a nanotube, changing the screw-sense of a helical molecule, and tying a protein knot). Our studies quantitatively demonstrate that the interactive VR environment allows users to complete sophisticated 3d spatial modelling tasks more quickly than they can using more conventional screen-based interfaces like mice or tablets, especially for tasks like protein knotting which are intrinsically 3d. We have now begun to extend this framework to accelerate progress in nanoscale molecular engineering areas including conformational mapping, drug-protein binding, [3] synthetic biology, and catalyst design. More broadly, our findings highlight the potential of VR in scientific domains where 3-dimensional dynamics matter, spanning scientific research, communication, and education.

  1. O Connor et al., Sampling molecular conformations and dynamics in a multi-user virtual reality framework”, 2018, Science Advances.
  2. https://vimeo.com/244670465.
  3. https://vimeo.com/296300796.

 

Free tickets are available, and refreshments will be provided, including beer.

Future Lightning Talks

We love to hear from you! Get in touch if you would like to give a 5 minute Lightning Talk at a future CCK on your latest research or give a quick demo of your latest programming project, or even to nominate someone you’d like to hear from (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’s 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-12

TL;DR: CCK-12, the next in our series of meetings for computational chemists, cheminformaticians, and molecular modelers, will be on Tuesday, September 4th, 2018, at 5 pm in the Seminar Room, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU. Free CCK-12 tickets are available.

 

Dear Friends and Colleagues,

Please join us for our next “Comp Chem Kitchen”, CCK-12, at 5-6 pm on Tuesday, September 4th, 2018, in the Seminar Room, Department of Biochemistry, South Parks Road, Oxford. We are  very pleased to announce Prof. Alessandro Contini from the Department of Pharmaceutical Sciences, Università degli Studi di Milano, Italy, will be speaking:

  • Prof. Alessandro Contini (Department of Pharmaceutical Sciences, Università degli Studi di Milano, Italy):Nwat-MMGBSA: mixing implicit and explicit solvation for a better prediction of relative binding energies“.

— MM-PBSA is a rather popular method, often used in binding energy calculations. Both strengths and weaknesses depend on the use of implicit solvation, that abolishes the energy fluctuations due to the rearrangement of water molecules but loses the contribution of explicit interactions between solute and solvent to the binding energy. Nwat-MMGBSA is a variant of MM-PB/GBSA thought to correct this last issue. Nwat-MMGBSA is based on including a fixed number of explicit water molecules that, in each frame of a molecular dynamics (MD) trajectory, are the closest to the ligand. The method provided improvements in the correlation between predicted and experimental binding energies in both ligand-receptor1 and protein-protein complexes,2 compared to standard MM-GBSA, with a negligible increase in cost. A set of scripts has been designed to automatically perform a structure based virtual screening workflow, including library preparation, docking, parameterization, MD and Nwat-MMGBSA rescoring, using non-commercial software.3 The full workflow, using an optimized setup, takes about 2h/ligand on a standard workstation equipped with a relatively cheap GPU card. In this talk, I will present some examples, discussing strengths, weaknesses and outlooks for this method.

1. Maffucci & Contini (2013) J. Chem. Theor. Comput., 9, 2706.
2. Maffucci & Contini, (2016) J. Chem. Inf. Model., 56, 1692.
3. Maffucci, Hu, Fumagalli & Contini, (2018) Front. Chem.https://doi.org/10.3389/fchem.2018.00043.

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]

Announcement: Course on Machine Learning for Chemoinformatics

Dr Martyn Winn would like to announce the following course:

Machine Learning for Chemoinformatics
Location: RAL, Harwell Campus
Dates: 6th – 10th August 2018
Registration fee:  academic £150, commercial £1000

The course covers all of the major methods in machine learning for classification and regression, with examples taken from problems in chemoinformatics. It has been designed for data analysts working in the pharmaceutical industry, but would also be useful to chemists interested in advanced data analysis. The course includes practical examples using commonly available Python packages.

For further information and to register, go to:

Cheers
Martyn

Dr. Martyn Winn
STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
E-mail: [email protected]       Skype: martyn.winn

Announcing the eCheminfo Oxford 2018 workshop

On behalf of the eCheminfo Network and Community of Practice, we would like to announce that the eCheminfo Oxford 2018 workshop is now open to registrations:

http://www.echeminfo.com/events/echeminfo-oxford-2018

It will be held 3-7 September, 2018, at Diamond House, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK.

In this one-week, hands-on workshop, leading modelling experts will introduce state-of-the-art and emerging modelling approaches and tools for all aspects of rational drug design and lead group work sessions, in which these tools will be applied on practical examples and case studies.

The case studies will be either provided by the participants (bring your own problems) or will be extracted from the keynote presentations.

In this way, the participants can directly apply their newly acquired knowledge to their own research, profit from specific advice by the experts and other participants and contribute to innovative approaches for all case studies.

The main topics covered by the workshop are:

  • virtual screening
  • ligand-based and structure-based drug design
  • bio- and cheminformatics
  • molecular dynamics simulation
  • drug delivery modelling
  • systems biology, and
  • biotech drug design.

Early-bird reduced rates available until 1 August, 2018.

Bursary Awards are available to support the registration costs of a selection of academic participants at the eCheminfo workshops.

CCK-11

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

(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

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.