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@fediscience.org @philbiggin@X
bigginlab.web.ox.ac.uk
@bigginlab@fediscience.org @philbiggin@X
bigginlab.web.ox.ac.uk
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.
Reposted by Phil Biggin
ChatGPT can now not only write, but also execute, RDKit code
www.linkedin.com/posts/nichol... #compchem
www.linkedin.com/posts/nichol... #compchem
ChatGPT can now use RDKit! | Nicholas Runcie | 15 comments
🔥 Blog Post 🔥 ChatGPT now has access to RDKit. You can ask the models to write and execute cheminformatics code directly in the chat. I have briefly played with these models, and my highlights are:
...
www.linkedin.com
June 5, 2025 at 5:40 AM
ChatGPT can now not only write, but also execute, RDKit code
www.linkedin.com/posts/nichol... #compchem
www.linkedin.com/posts/nichol... #compchem
Reposted by Phil Biggin
Federal funding for research is under unprecedented threat. How the public responds to this threat depends on whose stories they hear.
To increase public awareness of the value of federally-funded research, join the McClintock Letters Initiative. buff.ly/P85PopY
To increase public awareness of the value of federally-funded research, join the McClintock Letters Initiative. buff.ly/P85PopY
The McClintock Letters – Cornell Advancing Science and Policy Club
blogs.cornell.edu
June 3, 2025 at 4:12 PM
Federal funding for research is under unprecedented threat. How the public responds to this threat depends on whose stories they hear.
To increase public awareness of the value of federally-funded research, join the McClintock Letters Initiative. buff.ly/P85PopY
To increase public awareness of the value of federally-funded research, join the McClintock Letters Initiative. buff.ly/P85PopY
Reposted by Phil Biggin
This is such a big problem, perhaps especially in the decorous UK: scientists really don't want to appear unseemly or to "get political" in gatherings like this, even while what is happening (to NASA in this case) is cataclysmic. I've experienced it myself several times.
June 3, 2025 at 9:27 AM
This is such a big problem, perhaps especially in the decorous UK: scientists really don't want to appear unseemly or to "get political" in gatherings like this, even while what is happening (to NASA in this case) is cataclysmic. I've experienced it myself several times.
Reposted by Phil Biggin
Twenty case studies showing theoretical predictions in chemistry that were later confirmed experimentally. #CompChem 🧪
doi.org/10.1515/pac-...
doi.org/10.1515/pac-...
When theory came first: a review of theoretical chemical predictions ahead of experiments
For decades, computational theoretical chemistry has provided critical insights into molecular behavior, often anticipating experimental discoveries. This review surveys twenty notable examples from t...
doi.org
May 31, 2025 at 2:45 PM
Twenty case studies showing theoretical predictions in chemistry that were later confirmed experimentally. #CompChem 🧪
doi.org/10.1515/pac-...
doi.org/10.1515/pac-...
Reposted by Phil Biggin
Our new review article led by Jordan Kramer:
Platforms for studying cell–cell recognition by immune cells
onlinelibrary.wiley.com/doi/10.1111/...
Platforms for studying cell–cell recognition by immune cells
onlinelibrary.wiley.com/doi/10.1111/...
May 31, 2025 at 8:54 AM
Our new review article led by Jordan Kramer:
Platforms for studying cell–cell recognition by immune cells
onlinelibrary.wiley.com/doi/10.1111/...
Platforms for studying cell–cell recognition by immune cells
onlinelibrary.wiley.com/doi/10.1111/...
Great work from @haroldgrosjean.bsky.social and Kate Fieseler on how to extract SAR from HT crystallographic evaluation of fragment elaborations in crude reaction mixtures!
@oxfordbiochemistry.bsky.social
@diamondlightsource.bsky.social @oxfordstatistics.bsky.social
chemrxiv.org/engage/chemr...
@oxfordbiochemistry.bsky.social
@diamondlightsource.bsky.social @oxfordstatistics.bsky.social
chemrxiv.org/engage/chemr...
Structure-Activity-Relationships can be directly extracted from high-throughput crystallographic evaluation of fragment elaborations in crude reaction mixtures
Fragment hits serve as starting points for lead-like compound development. A common approach to advancing from fragments is to build structure-activity relationships (SARs) from close analogues. One ...
chemrxiv.org
May 28, 2025 at 8:02 AM
Great work from @haroldgrosjean.bsky.social and Kate Fieseler on how to extract SAR from HT crystallographic evaluation of fragment elaborations in crude reaction mixtures!
@oxfordbiochemistry.bsky.social
@diamondlightsource.bsky.social @oxfordstatistics.bsky.social
chemrxiv.org/engage/chemr...
@oxfordbiochemistry.bsky.social
@diamondlightsource.bsky.social @oxfordstatistics.bsky.social
chemrxiv.org/engage/chemr...
Looks useful!
Our joint paper with Wonpil Im lab is now available as a preprint:
"Dynamic Architecture of Mycobacterial Outer Membranes Revealed by All-Atom Simulations"
www.biorxiv.org/content/10.1...
"Dynamic Architecture of Mycobacterial Outer Membranes Revealed by All-Atom Simulations"
www.biorxiv.org/content/10.1...
May 27, 2025 at 5:14 PM
Looks useful!
Latest from the lab - Excellent work from Franco Viscarra! Franco used simulations to find the mode of action of a nicotinic "super-agonist" - then supported that with SDM and e-phys. Super-agonist, super-cool! Check it out here: www.biorxiv.org/content/10.1...
Allosteric Control of Super-Agonism in a Ligand-Gated Ion Channel
Ligand-gated ion channels open in response to the binding of an agonist. The agonist binding site is typically located tens of Angstroms away from the channel gate, which lies within the membrane and ...
www.biorxiv.org
May 26, 2025 at 11:45 AM
Latest from the lab - Excellent work from Franco Viscarra! Franco used simulations to find the mode of action of a nicotinic "super-agonist" - then supported that with SDM and e-phys. Super-agonist, super-cool! Check it out here: www.biorxiv.org/content/10.1...