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Irfan Alibay

@ialibay.bsky.social
101 followers 44 following 7 posts

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).

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Reposted by Irfan Alibay
MDAnalysis @mdanalysis.bsky.social · 13/07/2026
Excited to be in the next installment of the @omsf.io Stack Tour in Chicago August 27! Register to participate in a free hands-on tutorial delivered by MDAnalysis core developers, @ialibay.bsky.social and @micaelamatta.bsky.social. A full program and registration link are available at events.omsf.io
Open Molecular Software Foundation logo
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Reposted by Irfan Alibay
SBGrid Consortium @sbgrid.bsky.social · 09/02/2026
Join our software webinar on February 10th to hear from Alyssa Travitz of the @omsf.io on @openfree.energy: An Open Source Ecosystem for Calculating Free Energies. Tuesday, February 10, 2026 - 12:00pm ET Register here: buff.ly/N7AYdjp #SBGrid #Webinars #StructuralBiology
buff.ly
Webinars
The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…
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Reposted by Irfan Alibay
David L. Dotson @dotsdl.bsky.social · 14/01/2026
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 in alchemiscale v0.7
In October of this year we released alchemiscale v0.
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Reposted by Irfan Alibay
John Chodera @jchodera.bsky.social · 12/01/2026
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
openbind.ai
Home | openbind.uk
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Irfan Alibay @ialibay.bsky.social · 10/01/2026
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...
chemrxiv.org
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...
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Reposted by Irfan Alibay
Adrian Roitberg @adrianroitberg.bsky.social · 05/01/2026
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...
chemrxiv.org
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...
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Reposted by Irfan Alibay
Free Energy Workshop 2025 @feworkshop.bsky.social · 05/01/2026
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!
omsf.io
Alchemistry Workshop in Free Energy Methods for Drug Design - Alchemistry
Annual conference on Free Energy Methods in Drug Discovery
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Irfan Alibay @ialibay.bsky.social · 23/12/2025
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.
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Irfan Alibay @ialibay.bsky.social · 20/05/2025
Interested in learning more about @mdanalysis.bsky.social , simulation streaming and lots of cool molecular simulation tools? Come to the MDAnalysis 2025 UGM!
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Reposted by Irfan Alibay
Open Free Energy @openfree.energy · 15/05/2025
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
blog.omsf.io
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...
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Reposted by Irfan Alibay
Open Free Energy @openfree.energy · 04/02/2025
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...
Artistic rendering of a biochemical model: a small molecule ligand, shown as a ball-and-stick model colored by element, is bound in a pocket in a protein surface, shown as a space filling model colored off-white.
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Irfan Alibay @ialibay.bsky.social · 02/01/2025
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
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Irfan Alibay @ialibay.bsky.social · 27/12/2024
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!
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Irfan Alibay @ialibay.bsky.social · 03/12/2024
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 :)
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Reposted by Irfan Alibay
John Chodera @jchodera.bsky.social · 03/12/2024
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!
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