Irfan Alibay
@ialibay.bsky.social
Generally lost in alchemical space - Science Lead at Open Free Energy, Emeritus MDAnalysis core developer.
You can find me on github at @IAlibay and sometimes in Macclesfield (UK).
You can find me on github at @IAlibay and sometimes in Macclesfield (UK).
Reposted by Irfan Alibay
In October of 2025 we released alchemiscale v0.7.0, and followed this up with v0.7.1 and v0.7.2. We wanted to take a moment to highlight these releases, and the improvements they bring for @openfree.energy users!
alchemiscale.org/advancements...
#compchem #opensource #alchemistry #openscience
alchemiscale.org/advancements...
#compchem #opensource #alchemistry #openscience
advancements in alchemiscale v0.7
In October of this year we released alchemiscale v0.
alchemiscale.org
January 14, 2026 at 7:45 PM
In October of 2025 we released alchemiscale v0.7.0, and followed this up with v0.7.1 and v0.7.2. We wanted to take a moment to highlight these releases, and the improvements they bring for @openfree.energy users!
alchemiscale.org/advancements...
#compchem #opensource #alchemistry #openscience
alchemiscale.org/advancements...
#compchem #opensource #alchemistry #openscience
Reposted by Irfan Alibay
OpenBind is a new open science effort to dramatically increase the number of protein:ligand structures in the PDB, pairing this with high-quality affinity data to enable a new generation of predictive structure and affinity models for drug discovery. Check it out: openbind.ai
January 12, 2026 at 2:54 PM
OpenBind is a new open science effort to dramatically increase the number of protein:ligand structures in the PDB, pairing this with high-quality affinity data to enable a new generation of predictive structure and affinity models for drug discovery. Check it out: openbind.ai
Interested in what @omsf.io is up to? Here's a perspective on the role of open source in molecular modelling software and how the OMSF is developing an ecosystem of open tools: chemrxiv.org/engage/chemr...
The growing role of open source software in molecular modeling
The increasing importance and predictive power of modern molecular modeling, driven by physics- and machine learning-based methods, necessitates a new collaborative architecture to replace the isolate...
chemrxiv.org
January 10, 2026 at 2:50 AM
Interested in what @omsf.io is up to? Here's a perspective on the role of open source in molecular modelling software and how the OMSF is developing an ecosystem of open tools: chemrxiv.org/engage/chemr...
Reposted by Irfan Alibay
New Preprint dropped. LAMMPS + ANI, a super fast implementation of MLIPs. Highly parallel (> 1000 GPUS) and much faster than anything else out there ! Work done by the amazing @ignaciopickering.bsky.social, @nickterrel.bsky.social , and Jinze (Richard) Xue. chemrxiv.org/engage/chemr...
LAMMPS-ANI: Large Scale Molecular Dynamics Simulations
with ANI Neural Network Potential
Machine Learning Interatomic Potentials (MLIPs), trained with Quantum Mechanics data, can model
potential energy surfaces for molecular systems with very high accuracy and extreme speedups compared
to...
chemrxiv.org
January 5, 2026 at 9:11 PM
New Preprint dropped. LAMMPS + ANI, a super fast implementation of MLIPs. Highly parallel (> 1000 GPUS) and much faster than anything else out there ! Work done by the amazing @ignaciopickering.bsky.social, @nickterrel.bsky.social , and Jinze (Richard) Xue. chemrxiv.org/engage/chemr...
Reposted by Irfan Alibay
Exciting news! We have a new website: omsf.io/alchemistry
Your one-stop shop for everything related to our conference community. 🎉
BTW, registration is now open, so head over to secure your spot! We'll be sharing updates and details about the event.
Bookmark it as there's plenty more to come!
Your one-stop shop for everything related to our conference community. 🎉
BTW, registration is now open, so head over to secure your spot! We'll be sharing updates and details about the event.
Bookmark it as there's plenty more to come!
Alchemistry Workshop in Free Energy Methods for Drug Design - Alchemistry
Annual conference on Free Energy Methods in Drug Discovery
omsf.io
January 5, 2026 at 8:33 PM
Exciting news! We have a new website: omsf.io/alchemistry
Your one-stop shop for everything related to our conference community. 🎉
BTW, registration is now open, so head over to secure your spot! We'll be sharing updates and details about the event.
Bookmark it as there's plenty more to come!
Your one-stop shop for everything related to our conference community. 🎉
BTW, registration is now open, so head over to secure your spot! We'll be sharing updates and details about the event.
Bookmark it as there's plenty more to come!
My first corresponding author publication and it's a big one!
It's been a long and complicated process, but the team did an amazing job with it.
It's been a long and complicated process, but the team did an amazing job with it.
OpenFE is ready for production! chemrxiv.org/engage/chemr...
In collaboration with our industry partners, we ran benchmarking simulations of our hybrid-topology RBFE protocol on a large collection of both public and private protein-ligand binding datasets.
#compchem
In collaboration with our industry partners, we ran benchmarking simulations of our hybrid-topology RBFE protocol on a large collection of both public and private protein-ligand binding datasets.
#compchem
Large-scale collaborative assessment of binding free energy calculations for drug discovery using OpenFE
Accurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods, hav...
chemrxiv.org
December 23, 2025 at 12:38 AM
My first corresponding author publication and it's a big one!
It's been a long and complicated process, but the team did an amazing job with it.
It's been a long and complicated process, but the team did an amazing job with it.
Interested in learning more about @mdanalysis.bsky.social , simulation streaming and lots of cool molecular simulation tools? Come to the MDAnalysis 2025 UGM!
#mdaUGM2025 is officially happening! Abstracts and travel bursary applications are being accepted from now until the July 15, 2025 deadline: www.mdanalysis.org/2025/04/13/u....
🗓️ November 9-11, 2025
📍Tempe, Arizona, USA (and online)
#open-source-software #molecular #simulations #streaming
🗓️ November 9-11, 2025
📍Tempe, Arizona, USA (and online)
#open-source-software #molecular #simulations #streaming
May 20, 2025 at 9:26 PM
Interested in learning more about @mdanalysis.bsky.social , simulation streaming and lots of cool molecular simulation tools? Come to the MDAnalysis 2025 UGM!
Reposted by Irfan Alibay
If you weren't at @feworkshop.bsky.social in Boston last week, you missed Hannah Baumann giving the first sneak peek at results from our partner benchmarking study! Fortunately for you, Josh Horton wrote up a blog post about the early results: blog.omsf.io/the-free-ene...
#compChem
#compChem
The Free Energy of Everything: Benchmarking OpenFE
Written by: Josh Horton, PhD
Who is OpenFE and what do they do?
Open Free Energy (OpenFE) sits at the nexus of academia and industry. We are developing an open-source software ecosystem for alchem...
blog.omsf.io
May 15, 2025 at 2:00 PM
If you weren't at @feworkshop.bsky.social in Boston last week, you missed Hannah Baumann giving the first sneak peek at results from our partner benchmarking study! Fortunately for you, Josh Horton wrote up a blog post about the early results: blog.omsf.io/the-free-ene...
#compChem
#compChem
Reposted by Irfan Alibay
We're changing the field of #compchem by creating free and open-source software for performing alchemical free energy calculations. Our flagship protocol calculates relative binding free energies of protein-ligand systems. Try it out in your browser: colab.research.google.com/github/OpenF...
February 4, 2025 at 2:46 PM
We're changing the field of #compchem by creating free and open-source software for performing alchemical free energy calculations. Our flagship protocol calculates relative binding free energies of protein-ligand systems. Try it out in your browser: colab.research.google.com/github/OpenF...
Absolutely delighted to have been included @openuk.bsky.social 's 2025 honours list.
A big shout out to all the folks at @mdanalysis.bsky.social and @omsf.io for all their amazing work.
#opensource #openscience
A big shout out to all the folks at @mdanalysis.bsky.social and @omsf.io for all their amazing work.
#opensource #openscience
Happy New Year & congratulations to the UK-based open source software maintainers & open data leaders honoured in OpenUK's Honours List 25
See the full list https://buff.ly/40f8vwr
#openukhonours #maintainers #opendata #opensource
See the full list https://buff.ly/40f8vwr
#openukhonours #maintainers #opendata #opensource
January 2, 2025 at 4:56 PM
Absolutely delighted to have been included @openuk.bsky.social 's 2025 honours list.
A big shout out to all the folks at @mdanalysis.bsky.social and @omsf.io for all their amazing work.
#opensource #openscience
A big shout out to all the folks at @mdanalysis.bsky.social and @omsf.io for all their amazing work.
#opensource #openscience
Incredibly excited to see this work from Meghan Osato get to the preprint stage!
We knew that partial charge assignment with AM1BCC was unstable but we never would have guessed that it could cause such large issues with our free energy results!
We knew that partial charge assignment with AM1BCC was unstable but we never would have guessed that it could cause such large issues with our free energy results!
Evaluating the functional importance of conformer-dependent atomic partial charge assignment
Authors: Meghan Osato, Hannah Baumann, Jennifer Huang, Irfan Alibay, David Mobley
DOI: 10.26434/chemrxiv-2024-spw5s
Authors: Meghan Osato, Hannah Baumann, Jennifer Huang, Irfan Alibay, David Mobley
DOI: 10.26434/chemrxiv-2024-spw5s
December 27, 2024 at 8:47 AM
Incredibly excited to see this work from Meghan Osato get to the preprint stage!
We knew that partial charge assignment with AM1BCC was unstable but we never would have guessed that it could cause such large issues with our free energy results!
We knew that partial charge assignment with AM1BCC was unstable but we never would have guessed that it could cause such large issues with our free energy results!
Relicensing MDAnalysis was a major effort of ours, spanning over 3 years and far far too much of my time spent reading up on the the legal details of licenses. Major thanks to @orbeckst.bsky.social for pushing the process (and my often slow to act self) along :)
We released MDAnalysis 2.8.0 🚀 See the blog post www.mdanalysis.org/2024/11/22/r... . Highlights: (1) all code under the GNU Lesser General Public License, (2) new Guesser API, (3) general parallelization for analysis tools, (3) DSSP analysis class, (4) more MDAKits.
Release 2.8.0 of MDAnalysis · MDAnalysis
www.mdanalysis.org
December 3, 2024 at 8:36 PM
Relicensing MDAnalysis was a major effort of ours, spanning over 3 years and far far too much of my time spent reading up on the the legal details of licenses. Major thanks to @orbeckst.bsky.social for pushing the process (and my often slow to act self) along :)
Reposted by Irfan Alibay
CADD community, here's your chance to test how well your prediction models for affinity and ADMET *really* work in a real drug discovery program where all the data and protocols will be released openly!
We're excited to work with @omsf.io OpenADMET and @polarishub.io to bring you this blind predictive modeling community challenge!
If you're developing predictive models for drug discovery---potency or ADMET---here's your chance to test them prospectively on real discovery data from ASAP!
If you're developing predictive models for drug discovery---potency or ADMET---here's your chance to test them prospectively on real discovery data from ASAP!
🦠 We’re excited to announce our first competition in partnership with @asapdiscovery.bsky.social and @omsf.io!
Test your skills across three sub-challenges revolving around SARS-CoV-2 and MERS-CoV Mpro🧵
Full details: polarishub.io/competitions
Blog: polarishub.io/blog/antivir...
Test your skills across three sub-challenges revolving around SARS-CoV-2 and MERS-CoV Mpro🧵
Full details: polarishub.io/competitions
Blog: polarishub.io/blog/antivir...
December 3, 2024 at 4:47 PM
CADD community, here's your chance to test how well your prediction models for affinity and ADMET *really* work in a real drug discovery program where all the data and protocols will be released openly!