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.
You can find me on github at @IAlibay.
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!