OPIG’s growing immunoinformatics team continues to develop and openly distribute a wide variety of databases and software packages for antibody/nanobody/T-cell receptor analysis. Below is a summary of all the latest updates (follows on from v1.0 and v2.0).
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9th Joint Sheffield Conference on Cheminformatics
Over the next few days, researchers from around the world will be gathering in Sheffield for the 9th Joint Sheffield Conference on Cheminformatics. As one of the organizers (wearing my Molecular Graphics and Modeling Society ‘hat’), I can say we have an exciting array of speakers and sessions:
- De Novo Design
- Open Science
- Chemical Space
- Physics-based Modelling
- Machine Learning
- Property Prediction
- Virtual Screening
- Case Studies
- Molecular Representations
It has traditionally taken place every three years, but despite the global pandemic it is returning this year, once again in person in the excellent conference facilities at The Edge. You can download the full programme in iCal format, and here is the conference calendar:
Continue readingThe State of Computational Protein Design
Last month, I had the privilege to attend the Keystone Symposium on Computational Design and Modeling of Biomolecules in beautiful Banff, Canada. This conference gave an incredible insight into the current state of the protein design field, as we are on the precipice of advances catalyzed by deep learning.
Here are my key takeaways from the conference:
Continue readingBe a computational chemist and you must be a jack of all trades
Being a jack of all trades brings to mind someone who has extensive multidisciplinary expertise and is equipped with many tools in their toolbox to solve different problems. A jack of all trades is a great succinct description for computational chemists in drug discovery.
Recently I had a great conversation with Dr. Arjun Narayanan, a Senior Research Scientist at Vertex Pharmaceuticals and a jack of all trades as a computational chemist. In this blog post, I’ll describe what he does as a computational chemist, the problems he solves, and the new tools he’s looking forward to adding to his toolbox.
Experience at a Keystone Symposium
From 19th-22nd February I was fortunate enough to participate in the joint Keystone Symposium on Next-Generation Antibody Therapeutics and Multispecific Immune Cell Engagers, held in Banff, Canada. Now in their 51st year, the Keystone Symposia are a comprehensive programme of scientific conferences spanning the full range of topics relating to human health, from studies on fundamental bodily processes through to drug discovery.
Continue readingHappy 10th Birthday, Blopig!
OPIG recently celebrated its 20th year; and on 10 January 2023 I gave a talk just a day before the 10th anniversary of BLOPIG’s first blog post. It’s worth reflecting on what’s stayed the same and what’s changed since then.
Continue readingSome Musings on AI in Art, Music and Protein Design
When I started my PhD in late 2018, AI hadn’t really entered the field of de novo protein design yet – at least not in a big way. Rosetta’s approach of continually ranking new side chain rotamers on a fixed backbone was still the gold standard for the ‘structure-to-sequence’ problem. And of course before long we had AI making waves in the structure prediction field, eventually culminating in the AlphaFold2 we all know and love.
Now, towards the end of my PhD, we are seeing the emergence of new generative models that learn from existing pdb structures to produce sequences that will (or at least should) fold into viable, sensible and crucially natural-looking shapes. ProtGPT2 is a good example (https://www.nature.com/articles/s41467-022-32007-7), but there are several more. How long before these models start reliably generating not only shapes but functions too? Jury’s out, but it’s looking more and more feasible. Safe to say the field as a whole has evolved massively during my time as a graduate student.
Continue readingCode your own molecule sketcher in 4 easy steps!
Drawing molecules on your laptop usually requires access to proprietary software such as ChemDraw (link) or free websites such as PubChem’s online sketcher (link). However, if you are feeling adventurous, you can build your personal sketcher in React/Typescript using the Ketcher package!
Ketcher is an open-source package that allows easy implementation of a molecule sketcher into a web application. Unfortunately, it does require TypeScript so the script to run it cannot be imported directly into an HTML page. Therefore we will set up a simple React app to get it working.
The sketcher is very sleek and has a vast array of functionality, such as choosing any atom from the periodic table and being able to directly import molecules from either SMILES or Mol2/SDF file format into the sketcher. These molecules can then be edited and saved to a new file in the chemical file format of your choosing.
Continue reading5th Artificial Intelligence in Chemistry Symposium
The lineup for the Royal Society of Chemistry’s 5th “Artificial Intelligence in Chemistry” Symposium (Thursday-Friday, 1st-2nd September 2022) is now complete for both oral and poster presentations. It really is a fantastic selection of topics and speakers and it is clear this event is now a highlight of the scientific calendar. Our very own Prof. Charlotte M. Deane, MBE will be giving a keynote.
It marks a return to in-person meetings: it will be held at Churchill College, Cambridge, with a conference dinner at Trinity Hall.
More details are here: https://www.rscbmcs.org/events/aichem22/.
Registration for in person attendance is open until Monday 29th August 17:00 (BST).
It is also possible to register for virtual attendance; the meeting will be broadcast on Zoom.
CryoEM is now the dominant technique for solving antibody structures
Last year, the Structural Antibody Database (SAbDab) listed a record-breaking 894 new antibody structures, driven in no small part by the continued efforts of the researchers to understand SARS-CoV-2.
In this blog post I wanted to highlight the major driving force behind this curve – the huge increase in cryo electron microscopy (cryoEM) data – and the implications of this for the field of structure-based antibody informatics.
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