Phil Biggin
@philbiggin.bsky.social
Computational biochemist, interested in neuronal signalling at the atomic level and computer-aided drug design. All views my own.
bigginlab.web.ox.ac.uk
bigginlab.web.ox.ac.uk
Reposted by Phil Biggin
Have you always wanted to use CP2K but found the online manual too superficial and our JCP 2020 code review paper (doi.org/10.1063/5.00...) too theoretical? Then our new overview paper "The CP2K Program Package Made Simple" from the user's perspective is just right for you!
doi.org/10.1021/acs....
doi.org/10.1021/acs....
The CP2K Program Package Made Simple
CP2K is a versatile open-source software package for simulations across a wide range of atomistic systems, from isolated molecules in the gas phase to low-dimensional functional materials and interfac...
doi.org
January 19, 2026 at 8:11 PM
Have you always wanted to use CP2K but found the online manual too superficial and our JCP 2020 code review paper (doi.org/10.1063/5.00...) too theoretical? Then our new overview paper "The CP2K Program Package Made Simple" from the user's perspective is just right for you!
doi.org/10.1021/acs....
doi.org/10.1021/acs....
Reposted by Phil Biggin
🚀 Bottom line:
With careful filtering, co-folding predictions can indeed teach ML about binding affinity.
👉 Read the full JCIM paper: pubs.acs.org/doi/full/10....
Work with Aniket Magarkar
@boehringerglobal.bsky.social and @philbiggin.bsky.social @ox.ac.uk
(6/6)
With careful filtering, co-folding predictions can indeed teach ML about binding affinity.
👉 Read the full JCIM paper: pubs.acs.org/doi/full/10....
Work with Aniket Magarkar
@boehringerglobal.bsky.social and @philbiggin.bsky.social @ox.ac.uk
(6/6)
Can AI-Predicted Complexes Teach Machine Learning to Compute Drug Binding Affinity?
We evaluate the feasibility of using co-folding models for synthetic data augmentation in training machine learning-based scoring functions (MLSFs) for binding affinity prediction. Our results show th...
pubs.acs.org
January 20, 2026 at 7:27 PM
🚀 Bottom line:
With careful filtering, co-folding predictions can indeed teach ML about binding affinity.
👉 Read the full JCIM paper: pubs.acs.org/doi/full/10....
Work with Aniket Magarkar
@boehringerglobal.bsky.social and @philbiggin.bsky.social @ox.ac.uk
(6/6)
With careful filtering, co-folding predictions can indeed teach ML about binding affinity.
👉 Read the full JCIM paper: pubs.acs.org/doi/full/10....
Work with Aniket Magarkar
@boehringerglobal.bsky.social and @philbiggin.bsky.social @ox.ac.uk
(6/6)
Reposted by Phil Biggin
Very happy that our group has been able to contribute to this fantastic study. @astburycentre.bsky.social @astbury-bsl.bsky.social
A new paper by @thornsesholdlab.bsky.social reports photoswitchable ligands with wavelength-dependent, and concentration-independent, control of TRPC4/5 channels in live tissues
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Ideal efficacy photoswitching for chromocontrol of TRPC4/5 channel functions in live tissues - Nature Chemical Biology
Using chemical photoswitchable reagents to exert purely wavelength-dependent control over biological systems in deep tissue and in vivo requires a concentration-independent design paradigm. Here, such...
www.nature.com
January 17, 2026 at 5:08 PM
Very happy that our group has been able to contribute to this fantastic study. @astburycentre.bsky.social @astbury-bsl.bsky.social
Congrats to Jodie Collingridge on our latest reprint with Esther Becker:
"Structural mechanism of TRPC3 inhibition by a potent and selective antagonist" - we propose the binding mode of a TRPC3 selective antagonist and put forward an inhibition mechanism.
www.biorxiv.org/content/10.6...
"Structural mechanism of TRPC3 inhibition by a potent and selective antagonist" - we propose the binding mode of a TRPC3 selective antagonist and put forward an inhibition mechanism.
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 13, 2026 at 12:57 PM
Congrats to Jodie Collingridge on our latest reprint with Esther Becker:
"Structural mechanism of TRPC3 inhibition by a potent and selective antagonist" - we propose the binding mode of a TRPC3 selective antagonist and put forward an inhibition mechanism.
www.biorxiv.org/content/10.6...
"Structural mechanism of TRPC3 inhibition by a potent and selective antagonist" - we propose the binding mode of a TRPC3 selective antagonist and put forward an inhibition mechanism.
www.biorxiv.org/content/10.6...
Reposted by Phil Biggin
Now open: call for #postdoc fellowships in data-driven life science! 🧪
• Two tracks: Academic and Industry
• 22 funded projects (15 academic, 7 industrial)
Read more and apply ↓
www.scilifelab.se/data-driven/...
@kawresearch.bsky.social
• Two tracks: Academic and Industry
• 22 funded projects (15 academic, 7 industrial)
Read more and apply ↓
www.scilifelab.se/data-driven/...
@kawresearch.bsky.social
DDLS Research School Postdoc call 2026
Call for Academic and Industrial Postdoctoral Fellowships in Data-Driven Life Science 2026 Generic Description of the DDLS Postdoc Program The SciLifeLab and Wallenberg National Program for Data-Drive...
www.scilifelab.se
January 13, 2026 at 8:57 AM
Now open: call for #postdoc fellowships in data-driven life science! 🧪
• Two tracks: Academic and Industry
• 22 funded projects (15 academic, 7 industrial)
Read more and apply ↓
www.scilifelab.se/data-driven/...
@kawresearch.bsky.social
• Two tracks: Academic and Industry
• 22 funded projects (15 academic, 7 industrial)
Read more and apply ↓
www.scilifelab.se/data-driven/...
@kawresearch.bsky.social
Congratulations @haroldgrosjean.bsky.social and @kate-fieseler.bsky.social on their paper explaining how to extract SAR data from throughput crystallographic evaluation of fragment elaborations in crude reaction mixtures. Awesome work!
pubs.rsc.org/en/content/a...
pubs.rsc.org/en/content/a...
Structure–activity relationships can be directly extracted from high-throughput crystallographic evaluation of fragment elaborations in crude reaction mixtures
Fragment-based drug design offers multiple routes to advance from fragments. One approach is to build structure–activity relationships (SAR) from analogue series in direct-to-biology workflows. Analog...
pubs.rsc.org
January 13, 2026 at 9:50 AM
Congratulations @haroldgrosjean.bsky.social and @kate-fieseler.bsky.social on their paper explaining how to extract SAR data from throughput crystallographic evaluation of fragment elaborations in crude reaction mixtures. Awesome work!
pubs.rsc.org/en/content/a...
pubs.rsc.org/en/content/a...
Lovely to be part of this cool piece of work with Andrew Jones and Franco Viscarra -where we show the honey bee alpha5 receptor is sensitive to certain amines.
pubmed.ncbi.nlm.nih.gov/41388072/
pubmed.ncbi.nlm.nih.gov/41388072/
Characterisation of an unusual nicotinic acetylcholine receptor subtype preferentially sensitive to biogenic amines - PubMed
Nicotinic acetylcholine receptors (nAChRs) are best known for mediating the fast actions of acetylcholine. However, the spectrum of other neurotransmitters possibly acting on these receptors is not well understood. Here, we report that the α5 nAChR subunit of the honey bee, Apis mellifera, when expr …
pubmed.ncbi.nlm.nih.gov
December 14, 2025 at 8:33 PM
Lovely to be part of this cool piece of work with Andrew Jones and Franco Viscarra -where we show the honey bee alpha5 receptor is sensitive to certain amines.
pubmed.ncbi.nlm.nih.gov/41388072/
pubmed.ncbi.nlm.nih.gov/41388072/
Congrats to Wei-Tse Hsu on our latest paper with Aniket Magarkar @boehringerglobal.bsky.social where we look at how well co-folding models might be used in the context of data-augmentation for affinity prediction models.
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Can AI-Predicted Complexes Teach Machine Learning to Compute Drug Binding Affinity?
We evaluate the feasibility of using co-folding models for synthetic data augmentation in training machine learning-based scoring functions (MLSFs) for binding affinity prediction. Our results show th...
pubs.acs.org
December 10, 2025 at 3:55 PM
Congrats to Wei-Tse Hsu on our latest paper with Aniket Magarkar @boehringerglobal.bsky.social where we look at how well co-folding models might be used in the context of data-augmentation for affinity prediction models.
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Reposted by Phil Biggin
A new tutorial manuscript is out! 🚀 Making @plumed.org fly: a tutorial on optimizing performance, by Daniele Rapetti, @bonomimax.bsky.social @carlocamilloni.bsky.social @bussigio.bsky.social and Gareth Tribello. arxiv.org/abs/2511.02699
Making PLUMED fly: a tutorial on optimizing performance
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. Whi...
arxiv.org
November 5, 2025 at 8:16 AM
A new tutorial manuscript is out! 🚀 Making @plumed.org fly: a tutorial on optimizing performance, by Daniele Rapetti, @bonomimax.bsky.social @carlocamilloni.bsky.social @bussigio.bsky.social and Gareth Tribello. arxiv.org/abs/2511.02699
Pleasure to be part of this work www.pnas.org/doi/10.1073/... with Sandip Basak at NTU where we show asymmetric gating in GLIC!
Asymmetric gating of a homopentameric ion channel GLIC revealed by cryo-EM | PNAS
Pentameric ligand-gated ion channels (pLGICs) are vital neurotransmitter receptors
that are key therapeutic targets for neurological disorders. Alt...
www.pnas.org
October 23, 2025 at 4:24 PM
Pleasure to be part of this work www.pnas.org/doi/10.1073/... with Sandip Basak at NTU where we show asymmetric gating in GLIC!
Complete collection of the COSB edition on New Concepts in Drug Discoverythat Rod Hubbard and I edited is now online. My deepest thanks to all authors for their excellent articles!
www.sciencedirect.com/special-issu...
www.sciencedirect.com/special-issu...
July 16, 2025 at 10:32 AM
Complete collection of the COSB edition on New Concepts in Drug Discoverythat Rod Hubbard and I edited is now online. My deepest thanks to all authors for their excellent articles!
www.sciencedirect.com/special-issu...
www.sciencedirect.com/special-issu...
"R&D is the driver of domestic economic growth" and we also know that graduate students are the engine room of R&D. So why cut studentships? @wellcometrust.bsky.social
NEW WELLCOME REPORT
R&D is a driver of domestic economic growth, but there's so much more that strength in science can do for the UK and the world.
Our report sets out a wider narrative for UK R&D, and why the UK needs to move on from 'science superpower'
wellcome.org/reports/uk-g...
R&D is a driver of domestic economic growth, but there's so much more that strength in science can do for the UK and the world.
Our report sets out a wider narrative for UK R&D, and why the UK needs to move on from 'science superpower'
wellcome.org/reports/uk-g...
The Global Partner of Choice for R&D | Report | Wellcome
This report outlines the importance of research and development (R&D) for the UK, emphasising its role in economic growth, global reputation and national security amidst changing geopolitical landscap...
wellcome.org
July 16, 2025 at 10:29 AM
"R&D is the driver of domestic economic growth" and we also know that graduate students are the engine room of R&D. So why cut studentships? @wellcometrust.bsky.social
Reposted by Phil Biggin
My wonderful colleage Colin Kleanthous is raising money for the MND association. Please support Colin in this worthy endeavor! www.justgiving.com/page/colin-k...
(Please repost!)
(Please repost!)
Colin Kleanthous' fundraiser for Motor Neurone Disease Association
Help Colin Kleanthous raise money to support Motor Neurone Disease Association
www.justgiving.com
July 15, 2025 at 7:21 AM
My wonderful colleage Colin Kleanthous is raising money for the MND association. Please support Colin in this worthy endeavor! www.justgiving.com/page/colin-k...
(Please repost!)
(Please repost!)
Latest pp with Aniket Magarkar @boehringerglobal.bsky.social - We evaluated the potential of co-folding models to generate synthetic protein–ligand complexes for training machine learning-based scoring functions. arxiv.org/abs/2507.07882. Btw - Wei-Tse Hsu at this GRC tinyurl.com/3knvp3wn
Can AI-predicted complexes teach machine learning to compute drug binding affinity?
We evaluate the feasibility of using co-folding models for synthetic data augmentation in training machine learning-based scoring functions (MLSFs) for binding affinity prediction. Our results show th...
arxiv.org
July 14, 2025 at 10:16 AM
Latest pp with Aniket Magarkar @boehringerglobal.bsky.social - We evaluated the potential of co-folding models to generate synthetic protein–ligand complexes for training machine learning-based scoring functions. arxiv.org/abs/2507.07882. Btw - Wei-Tse Hsu at this GRC tinyurl.com/3knvp3wn
Reposted by Phil Biggin
Job advert to come and work with me on tuberculosis closes tomorrow (Friday) at noon!
Part of #OxCOD4TB
bit.ly/4ndKOhF
@ndm.ox.ac.uk @modmedmicro.bsky.social
@oxfordbrc.bsky.social
Part of #OxCOD4TB
bit.ly/4ndKOhF
@ndm.ox.ac.uk @modmedmicro.bsky.social
@oxfordbrc.bsky.social
Job Details
bit.ly
July 3, 2025 at 1:33 PM
Job advert to come and work with me on tuberculosis closes tomorrow (Friday) at noon!
Part of #OxCOD4TB
bit.ly/4ndKOhF
@ndm.ox.ac.uk @modmedmicro.bsky.social
@oxfordbrc.bsky.social
Part of #OxCOD4TB
bit.ly/4ndKOhF
@ndm.ox.ac.uk @modmedmicro.bsky.social
@oxfordbrc.bsky.social
Was a great pleasure to work with Rod Hubbard on this COSB issue on drug discovery. Thanks to all the authors who contributed!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Editorial overview by Philip Biggin (University of Oxford) and Roderick Hubbard (University of York) 2025 issue of Current Opinion in Structural Biology - New Concepts in Drug Discovery (2025)
www.sciencedirect.com
July 2, 2025 at 12:50 PM
Was a great pleasure to work with Rod Hubbard on this COSB issue on drug discovery. Thanks to all the authors who contributed!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Phil Biggin
Opportunity for computational chemist at Syngenta (Bracknell UK) #agrochem #CompChem #cheminformatics #AI #ML #UKChemJobs #ChemJobs #chemsky 🧪
jobs.syngenta.com/job/principa...
jobs.syngenta.com/job/principa...
Principal Scientist - Computational Chemistry
jobs.syngenta.com
July 1, 2025 at 6:32 AM
Opportunity for computational chemist at Syngenta (Bracknell UK) #agrochem #CompChem #cheminformatics #AI #ML #UKChemJobs #ChemJobs #chemsky 🧪
jobs.syngenta.com/job/principa...
jobs.syngenta.com/job/principa...
💯
Science minister Patrick Vallance has warned that “curiosity-driven” research is one of the “easiest” areas for governments to cut, but stressed it must be “protected and grown” alongside improving the UK’s applied research base
#Metascience2025
www.timeshighereducation.com/news/basic-r...
#Metascience2025
www.timeshighereducation.com/news/basic-r...
Basic research funding ‘must be protected and grown’ - Vallance
Funding for curiosity-driven research ‘easiest area’ for governments to cut, warns science minister
www.timeshighereducation.com
June 30, 2025 at 3:33 PM
💯
Reposted by Phil Biggin
Opportunity for biophysical scientist at Vernalis (Cambridge UK) #biochem #biophysics #assay #AnalChem #PhysChem #UKChemJobs #ChemJobs #chemsky 🧪
www.vernalis.com/vacancies/sc...
www.vernalis.com/vacancies/sc...
Scientist – Biophysical
Vernalis collaborates with a wide range of organisations to enable drug discovery programs through both short- and long-term projects
www.vernalis.com
June 20, 2025 at 7:16 AM
Opportunity for biophysical scientist at Vernalis (Cambridge UK) #biochem #biophysics #assay #AnalChem #PhysChem #UKChemJobs #ChemJobs #chemsky 🧪
www.vernalis.com/vacancies/sc...
www.vernalis.com/vacancies/sc...
Reposted by Phil Biggin
Too cool to be true? 😎 Nope! GlycoShape ReGlyco runs on PyMol through the GlycoMe interface 🥰😍 check out this fab #glycotime tool from Hiren @glyco.me and Ojas @ojas-singh.bsky.social ⤵️🥳🥳🥳🎉🎉
Well, it turns out that you can actually make PyMOL do quite a lot of stuff. Here's the full workflow, integrating the amazing ReGlyco into PyMOL to re-glycosylate the LDLA linker. There's some serious magic needed to get it running as fast as it is within PyMOL. @elisafadda.bsky.social
June 11, 2025 at 6:33 AM
Too cool to be true? 😎 Nope! GlycoShape ReGlyco runs on PyMol through the GlycoMe interface 🥰😍 check out this fab #glycotime tool from Hiren @glyco.me and Ojas @ojas-singh.bsky.social ⤵️🥳🥳🥳🎉🎉
Long overdue,but this is a huge relief and great news for computational research in the UK!
www.ft.com/content/b1e9...
www.ft.com/content/b1e9...
Edinburgh supercomputer to get £750mn in UK spending review
Funding comes after Labour initially pulled money for the project last July
www.ft.com
June 10, 2025 at 9:05 PM
Long overdue,but this is a huge relief and great news for computational research in the UK!
www.ft.com/content/b1e9...
www.ft.com/content/b1e9...
Reposted by Phil Biggin
First full day of the Summer School on Biomolecular Simulations 2025 in Sardinia 😎 🏖️
It's mostly about #moleculardynamics and #GROMACS with lectures and hands-on tutorials
Check out these useful MD tricks from Prof. Berk Hess👇
It's mostly about #moleculardynamics and #GROMACS with lectures and hands-on tutorials
Check out these useful MD tricks from Prof. Berk Hess👇
June 9, 2025 at 8:15 PM
First full day of the Summer School on Biomolecular Simulations 2025 in Sardinia 😎 🏖️
It's mostly about #moleculardynamics and #GROMACS with lectures and hands-on tutorials
Check out these useful MD tricks from Prof. Berk Hess👇
It's mostly about #moleculardynamics and #GROMACS with lectures and hands-on tutorials
Check out these useful MD tricks from Prof. Berk Hess👇
Reposted by Phil Biggin
So much waste and harm could be avoided if we just treated these as fragile, dangerous tools suited for very specialized use cases, like we do with lasers and circular saws, and not as magic thinking beans
Cutting-edge AI models ‘collapse’ in face of complex problems, Apple study finds
Cutting-edge AI models ‘collapse’ in face of complex problems, Apple study finds
‘Pretty devastating’ paper raises doubts about race to reach stage of AI at which systems match human intelligence
Apple researchers have found “fundamental limitations” in cutting-edge artificial intelligence models, in a paper raising doubts about the technology industry’s race to develop ever more powerful systems.
Apple claimed in a paper published at the weekend that large reasoning models (LRMs) – an advanced form of AI – faced a “complete accuracy collapse” when presented with highly complex problems. Continue reading...
www.theguardian.com
June 9, 2025 at 9:52 PM
So much waste and harm could be avoided if we just treated these as fragile, dangerous tools suited for very specialized use cases, like we do with lasers and circular saws, and not as magic thinking beans
Reposted by Phil Biggin
www.ft.com/content/8778...
Kudos to Andrea Sella for taking a stand against @royalsociety.org’s inaction over Elon Musk FRS
Kudos to Andrea Sella for taking a stand against @royalsociety.org’s inaction over Elon Musk FRS
Royal Society prize winner returns award in protest over Elon Musk
Andrea Sella is latest scientist to express dismay over UK science academy’s refusal to criticise tech billionaire
www.ft.com
June 10, 2025 at 5:17 AM
www.ft.com/content/8778...
Kudos to Andrea Sella for taking a stand against @royalsociety.org’s inaction over Elon Musk FRS
Kudos to Andrea Sella for taking a stand against @royalsociety.org’s inaction over Elon Musk FRS
Reposted by Phil Biggin
We'd be a lot better off if we dump the religions and accept this.
June 7, 2025 at 2:58 PM
We'd be a lot better off if we dump the religions and accept this.