|UK-QSAR Spring 2023
|The UK-QSAR and Cheminformatics Group
|Welcome to the Spring 2023 UK-QSAR Newsletter!
The Spring UKQSAR & Cheminformatics Group Meeting will be held at the Wellcome Genome Campus, Hinxton, Cambridge, on Thursday 20th April 2023. The meeting is organised jointly by EMBL-EBI and Sosei Heptares, and as always, is free, although registration is required. Registration is nearly full so please book soon if you plan to attend, and if you no longer need your spot do let us know so we can release it to others.
UPDATE: In-person registration full as of 10th April, but you can still register for online attendance or to join the waiting list!
More details about the meeting are below, including the optional pre-meeting dinner, as well as an article on ChatGPT and information on current job openings and upcoming meetings which may be of interest.The provisional date/venue for our autumn meeting is Thursday September 14th, at Liverpool John Moores University.As ever, please send any feedback or suggestions you have for future newsletters to Susan Boyd at email@example.com.
Spring Meeting Information
The theme this time is “Learning from data” and the morning session will revolve around three of the most relevant databases for our fields, PubChem, ChEMBL and the Cambridge Structural Database. There will also be sessions on protein structure-based techniques (including use of AlphaFold, and ML for virtual screening) and reaction informatics (including applications of Enamine REAL, and machine learning).
Registration is now open. Please register using the following link: https://www.eventsforce.net/embl/93/register. Only registered participants will be allowed to attend. Please let us know if you can no longer attend, so that we can free up your place, as the meeting is nearly full, and we expect it to be over-subscribed.Registration closes at 23.30 BST on the 10th April.
UPDATE: In-person registration full as of 10th April, but you can still register for online attendance or to join the waiting list!UPDATE: PRE-MEETING DINNERAs it is the tradition for all UK-QSAR meetings, we would like to offer the opportunity to meet in the evening before for an informal dinner. It is an opportunity to meet some of the meeting organizers, but more importantly, to meet other people from the same field.
For this occasion, we are thinking of going to the Prezzo restaurant in central Cambridge at 7pm, and for those interested, we can later go to a nearby pub. Note that you will have to pay for yourselves.If you are interested, please reply to Noel O’Boyle (Noel.O’Boyle-at-SoseiHeptares.com) or Nicolas Bosc (nbosc-at-ebi.ac.uk ) by the end of the week so they can book a table.
LOCATION AND TRAVELThe EMBL-EBI building is located on the Wellcome Genome Campus.
Photo by Edmund Sumner, courtesy of https://archello.com/project/embl-ebi-south-building. Google map directions
Please find information on traveling to EMBL-EBI on their website.
FOR POSTER PRESENTERS
As part of the registration process, you will be offered to submit an abstract. This will be reviewed by the organising committee, who will then confirm whether you will be able to present a poster. If you would like to present a poster, please register as soon as you can to allow us time to review your abstract and you time to create your poster before the day.Key dates and information:Abstracts can only be submitted to the organising committee at the time of registrationAbstracts must NOT EXCEED 300 CHARACTERS, and must be uploaded as .pdf files
You will be notified by 5pm on 12TH APRIL if you are successful. All posters need to be PRE-PRINTED as A1 size (23.4 x 33.1 inches / 594 x 841 mm). Posters must be brought along ready for 9AM BST on the day of the meeting to allow enough set-up time. The event organisers will attach all posters to the boards on the day.
EBI recommend the following hotels. In distance order from the venue, starting with the closest first.
Hinxton Hall Conference Centre (located on campus)Please note that Hinxton Hall has limited availability for this date so delegates are advised to book as soon as possible.
Red Lion Hinxton (5 minute walk from campus)
HOLIDAY INN EXPRESS CAMBRIDGE-DUXFORD M11, JCT.10 (a short taxi ride away from campus) For more information on accommodation please see their website here.
9:30 Open registration, coffee/tea
10:15 Welcome and opening remarks Andrew R Leach
Session 1 Data for Advanced Research
10:30 PubChem: a wealth of information for your research Evan Bolton (PubChem)
11:00 EMBL-EBI’s Chemical Biology Resources for Drug Discovery – what does the future hold? Barbara Zdrazil (EMBL-EBI)
11:30 Learning from the Cambridge Structural Database Isaac Sugden (CCDC)
12:00 Lunch & poster session
Session 2 Learning from data – Protein structure-based techniques
1:30 Applications of AlphaFold and Generative Molecular Design for GPCR SBDD Brian Bender (Sosei Heptares)
2:00 Expanding the target coverage and accuracy of virtual screening in the age of machine learning Marton Vass (Schrodinger)
Session 3 Learning from data – Reaction informatics
15:00 Making virtual REAL: creation and application Yurii Moroz (ChemSpace)
15:30 TBA Lucy van Dijk (Vertex)
16:00 Machine Learning around the Design-Make-Test Cycle Marwin Segler (Microsoft)
16:30 Concluding remarks, poster prize winner announcement and close Chris de Graaf/Noel O’Boyle
ABSTRACTS & PRE-READING
The speakers have provided the following abstracts and references which might be of interest ahead of their talks.
Evan Bolton, Head Chemistry Program (National Library of Medicine)
PubChem: a wealth of information for your research
PubChem is a massive resource. An effective strategy to access what you need requires a little knowledge and imagination. This talk will give you a broad overview of major ways to access information from PubChem whether you are a beginner or an expert or whether you are a technophobe or a technophile. In addition, this talk will give you some illustrative examples to help you get a sense of how PubChem can help meet your research needs.
Barbara Zdrazil, ChEMBL Coordinator (EMBL-EBI)
EMBL-EBI’s Chemical Biology Resources for Drug Discovery – what does the future hold?
The Chemical Biology Services’ Team at the European Bioinformatics Institute manages the ChEMBL database of quantitative small-molecule bioactivity data used in drug discovery; SureChEMBL, for patent information; UniChem, a convenient way to cross-reference multiple databases using chemical structure; and ChEBI, a database of small molecules relevant to biology. All our resources are open and follow FAIR principles. Recognising their global importance, ChEMBL and ChEBI have recently been designated as Global Core Biodata Resources (https://globalbiodata.org/scientific-activities/global-core-biodata-resources/).Over time these resources have grown in complexity and size, and they have been used by the drug discovery and related communities to answer practical science questions. Example applications include the identification of tool compounds for potential therapeutic targets, novelty evaluation, target profiling for bioactive compounds and many more. ChEMBL is also very widely used in data science and in the development, validation, and application of AI/ML methods.In this talk, we will describe the evolution of our resources, provide some practical examples of their usage, and outline some of the new functionalities and plans for the future.
Márton Vass, Principal Applications Scientist (Schrodinger)
Expanding the target coverage and accuracy of virtual screening in the age of machine learning
Machine learning technologies are now influencing all stages of the drug discovery process. Since the advent of AlphaFold2 it has been an open question whether this or derived methods could provide starting points for structure-based drug discovery techniques. We have investigated the usability of AlphaFold2 models in virtual screening experiments using the unrefined models or their binding sites refined with Schrödinger’s IFD-MD tool. We show that unrefined structures, on average, provide enrichments on par with apo crystal structures, whereas refined structures can provide enrichments close to their holo counterparts. A combination of IFD-MD and FEP technologies can also be used on homology models and AlphaFold2 structures to uncover compound binding modes in novel targets and for structure-based hit expansion and lead optimization.
Yurii Moroz, CEO (ChemSpace)Making virtual REAL: creation and application.
ChatGPT – FRIEND OR FOE?
Susan Boyd, CompChem Solutions Ltd
There’s been so much hype around ChatGPT (and its peers) recently – but how might it impact our lives as computational scientists, going forward? Is it a tool we can use to our benefit, or an existential threat to our current livelihoods?Already, it can pass some medical exams, law exams and some pre-university high school exams. It can write essays, poems (some definitely better than others!) and indeed code. I asked it to write a newsletter for the UK-QSAR and Cheminformatics Society. This is what it produced.
“We hope this newsletter finds you well. As always, we have some exciting updates and announcements to share with you regarding upcoming events and activities.First, we are pleased to announce that the next UK-QSAR and Cheminformatics Society Meeting will be taking place on September 15-16, 2023, at the University of Cambridge. This year’s meeting will feature a range of talks and presentations from leading researchers in the fields of QSAR and cheminformatics, as well as ample opportunities for networking and collaboration. Registration for the meeting will open in the coming months, so be sure to mark your calendars and stay tuned for more information.In addition to the meeting, we have several other events and activities planned for the coming months. These include:A series of virtual workshops and webinars focused on various topics in QSAR and cheminformatics. These workshops will be led by experts in the field and will provide attendees with the opportunity to learn new skills and techniques, as well as to network with other researchers and professionals.A virtual poster session for early-career researchers and students to showcase their research in the fields of QSAR and cheminformatics. This session will provide a valuable opportunity for young researchers to gain exposure for their work and to receive feedback from their peers and more experienced researchers.A mentoring program for early-career researchers and students. This program will pair mentees with experienced researchers and professionals in the field, providing them with guidance, support, and advice as they navigate their careers in QSAR and cheminformatics.As always, we welcome your feedback and input regarding these events and activities, as well as any other suggestions you may have for how we can best serve the needs and interests of our members. Please don’t hesitate to get in touch with us if you have any questions or comments.”
Ok, not a bad job as a first attempt, and some nice ideas in there (mentoring programme anyone?), but I don’t think I’ll be usurped in the immediate future!)
I also asked it: “Can you write a Python script to parse a PDB file and replace the b-factors in the file with new ones, supplied as a csv file?” The reply? A working piece of code:
Nice….but again, is this new entity a friend or a foe? For now, we can contain it, we can use it to perform specific coding tasks or to write poetry or prose but where will it all go next? If Elon Musk and over 1,000 of his AI expert buddies are right, we might want to pause and think about ways to develop AI safely. If the current rate of development/learning continues, these systems may well become just a bit more sinister!
Principal Scientist, Computational Chemistry, Domainex, Cambridge, UK, https://ukqsar.org/index.php/2023/02/01/principal-scientist-computational-chemistry-domainex/
Drug Hunter Molecular Architect, Evotec, Abingdon, UK, https://evotecgroup.wd3.myworkdayjobs.com/en-US/Evotec_Career_Site/job/Abingdon/Senior-Scientist-1—Team-Leader_REQ-06570?Location_Country=29247e57dbaf46fb855b224e03170bc7
Associate Principal/Principal Scientist Computational Chemistry, Sygnature, Alderley Park, UK, https://jobs.lever.co/sygnaturediscovery/7e783c33-da9f-466b-8359-57f165bc5beb
Senior Scientist Computational Chemistry, Sygnature, Nottingham/Alderley Park, UK, https://jobs.lever.co/sygnaturediscovery/f01dad1d-92d3-4e29-9cb1-4b9dee830a40
Application Scientist, Optibrium, Cambridge, UK, https://optibrium.com/careers/
Cheminformatics – Senior Scientist, LifeArc, Stevenage or Edinburgh, UK https://lifearc.livevacancies.co.uk/#/job/details/55
Assistant Professor in Computational Chemistry/Data Science , Durham University, Durham, UK
Postdoc Positions, AI in Drug Discovery, University of Sheffield, Sheffield, UK
Various positions, Cresset, Litlington, UK, https://www.cresset-group.com/about/careers/open/
Machine learning scientist, Astex, Cambridge, UK, https://www.cloudonlinerecruitment.co.uk/Astex/VacancyDetails.aspx?FromSearch=True&MenuID=&VacancyID=41
Various positions, AstraZeneca, Cambridge UK or Gothenburg Sweden, https://careers.astrazeneca.com/location/united-kingdom-jobs/7684/2635167/2
The following meetings may be of interest to our readers:
CCG UGM & Conference Europe, 30th May – 2nd June 2023, Munich, https://www.chemcomp.com/UGM-2023-Europe.htm
Cambridge Cheminformatics Meeting, 7th June 2023, Cambridge UK, http://c-inf.net
Ninth Joint Sheffield Conference on Chemoinformatics – Registration Open
Sheffield, UK, 19-21st June 2023, https://cisrg.shef.ac.uk/shef2023
Gordon Research Conference (GRC): Data Analytics and Computational Modeling for Next Generation Molecular Design, West Dover, VT, 16-21st July 2023, https://www.grc.org/computer-aided-drug-design-conference/2023
RDKit UGM, Mainz, Germany and Virtual Event, 20-22 September 2023, https://www.eventbrite.com/e/12th-rdkit-ugm-2023-tickets-566636253287
UKQSAR Autumn 2023 Meeting, 14th October 2023, Liverpool JMU (TBC), details will be posted to https://ukqsar.org/index.php/category/meetings/ when available