Irfan Alibay

RSE @ OMSF (biomol MD, free energy calcs, etc...), @MDAnalysis and @openfreeenergy core developer | he/him - views are my own

[Irfan Alibay @HighSpeedMode]

@mdanalysis #shiny sticker travelling journey: attending @orbeckst' COMP talk at s401d

[a gentle bree(zeph) @hearmyqueer]

@HighSpeedMode @mdanalysis @ACSCOMP Love a sticker that has travelled more than I have 😂

[MDAnalysis @mdanalysis.bsky.social @mdanalysis]

Are you a new or prospective MDAnalysis user?

Join us for our online training workshop for a basic introduction to MDAnalysis and hands-on tutorials!

🗓️ October 25, 15:00 UTC
🔗 Apply by September 30: https://t.co/b2ufOzLFS9

[Vytas @VytasGapsys]

The 2024 edition of the Free Energy Workshop will take place in Leiden, Netherlands, 13-15th May, 2024!
We have not yet opened registration, but you can already book the dates in your calendars.
Keep an eye on the wiki for further information: https://t.co/OGRFzVzLH7
#alchemy2024

[Irfan Alibay @HighSpeedMode]

Awesome work by @mikehenry42, alongside his previous push for py3.11 we can finally unblock a lot of the downstream ecosystem!

[Mike Henry 🌈🏳️‍⚧️ @mikehenry42]

Happy to announce @ambermdprog Ambertools 23 now has an osx-arm64 build on @condaforge 🚀

Now you can install ambertools without having to use Rosetta 2 emulation 🎉

Big thanks to @mwt_dev @jaime_rgp @ghutchis @hainm_comp @isuru_f for all of their help! 🙌

A few details 🧵

[Wendy Anne Warr @WendyAnneWarr]

#shef2023 https://t.co/u8ZgeZhb73

[Irfan Alibay @HighSpeedMode]

@AravindaMunasin @agrossfield @D_Lukauskis I should clarify, MM-(G/P)BSA have their place in a free energy estimation workflow. Indeed we've found the Nwat approach to be reasonably good at retrospective evaluations of fragment enumeration. BUT folks shouldn't ignore error bars in predictions.

[Antonia Mey @ppxasjsm]

🔥off the Arxiv press: SILVR a generative diffusion model for molecule generation from X-ray fragment data: https://t.co/iId6qrV8ag

✅ Conditioning for X-ray fragments
✅ Linking and merging X-ray fragments
✅ Molecules fit in binding site
❌ No retraining needed

[Tyler Reddy @Tyler_Reddy]

My team is recruiting an organic chemistry postdoc at LANL. Feel free to contact me directly.

[Irfan Alibay @HighSpeedMode]

@Biocheming @mdanalysis @JennaSwarthout be reasonably easy to implement. We would definitely be happy to see such a contribution to the code base if folks find it useful.

Our guesser infrastructure is also in progress of being completely updated for the 3.0 release, which should make things easier [2/2]

[Irfan Alibay @HighSpeedMode]

@Biocheming @mdanalysis @JennaSwarthout By default we try not to guess for folks, there are several corner cases where that can go wrong, for example if you use HMR or if you have a coarse grained system. We do have a means to guess elements from types: https://t.co/VVHJycuLcC and guessing from a mass dictionary [1/2]

[Irfan Alibay @HighSpeedMode]

@Biocheming @mdanalysis @JennaSwarthout Yes! Just use the `element` keyword. See https://t.co/bGnsfMJDGx for more details.

[MDAnalysis @mdanalysis.bsky.social @mdanalysis]

MDAnalysis will participate in #GSOC 2023! If you have some experience with #MD or other simulations at the molecular scale and if you like #coding to solve problems in #physics #chemistry #compchem #biochemistry #materialsscience is your thing: read https://t.co/fgoFpOPJJ4

[Irfan Alibay @HighSpeedMode]

Link to the poster if you don't happen to be at #bps2023 https://t.co/wFUuOglJms

[Irfan Alibay @HighSpeedMode]

Please come by for a chat! I'll be there during breaks throughout the day too!

[Fiona Naughton @ExplainedByCats]

Last year, @MDAnlaysis released a whitepaper outlining our proposed "MDAKits" -> https://t.co/G6YDjjjHPa

For those at #bps2023, hear more at @HighSpeedMode's poster(B446) on MDA today

But first, let's take a quick walk through MDAKits+the idea behind them- with some cute cats!

[Irfan Alibay @HighSpeedMode]

@jandom_random @ExplainedByCats Much worse UX, but probably much better validation? ;)

[Irfan Alibay @HighSpeedMode]

Also we have stickers and cat branded business cards!

[Irfan Alibay @HighSpeedMode]

@Dummyinresearch @ExplainedByCats @mdanalysis @lilyminium @orbeckst We do have a contribution guide in our user documentation: https://t.co/NAEo7Ycaw5

We always welcome any additions/comments/suggestions on how we can improve. Please do open up an issue: https://t.co/dGPFqP8rpJ

[Irfan Alibay @HighSpeedMode]

@mia_rosenfeld @ExplainedByCats @mdanalysis @lilyminium @orbeckst That sounds awesome, we're in 6A this morning if you want to trade!

[Fiona Naughton @ExplainedByCats]

Attending #BPS2023 and want to become the proud owner of a shiny new @mdanalysis sticker or fridge magnet? Come find me (look for the blue hair 😜 ), @HighSpeedMode, @lilyminium or @orbeckst !

[Irfan Alibay @HighSpeedMode]

@ExplainedByCats @mdanalysis @lilyminium @orbeckst Come see us at the @mdanalysis poster on Tuesday! Hall BC B446 @ 13:45