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Irfan Alibay
826 posts
Irfan Alibay
@HighSpeedMode
RSE @ OMSF (biomol MD, free energy calcs, etc...), @MDAnalysis and @openfreeenergy core developer | he/him - views are my own
England, United Kingdom 加入时间 Haziran 2009
322 关注435 粉丝
Irfan Alibay 已转推
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: eventbrite.com/e/681631767967
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Irfan Alibay 已转推
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: alchemistry.org/wiki/2024_Work…
#alchemy2024
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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 🧵
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Irfan Alibay 已转推
@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.
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@HighSpeedMode @agrossfield @D_Lukauskis I "was" a skeptic of MMGBSA/PBSA. Then I realized that as long as I benchmark against a dataset for a given target, this is a good method for ranking/screening. It does reasonably well for ranking even with crazy numbers.
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Irfan Alibay 已转推
🔥off the Arxiv press: SILVR a generative diffusion model for molecule generation from X-ray fragment data: arxiv.org/abs/2304.10905
✅ Conditioning for X-ray fragments
✅ Linking and merging X-ray fragments
✅ Molecules fit in binding site
❌ No retraining needed
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Irfan Alibay 已转推
My team is recruiting an organic chemistry postdoc at LANL. Feel free to contact me directly.
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@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]
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@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: docs.mdanalysis.org/1.1.1/document… and guessing from a mass dictionary [1/2]
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We welcome @JennaSwarthout as the new #CommunityManager for @mdanalysis, which will enable us to expand our mentoring, teaching and community engagement efforts!
#womenintech #DiversityandInclusion
mdanalysis.org/2023/03/14/pro…
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@Biocheming @mdanalysis @JennaSwarthout Yes! Just use the `element` keyword. See #simple-selections" target="_blank" rel="nofollow noopener">docs.mdanalysis.org/stable/documen… for more details.
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@mdanalysis @JennaSwarthout Is it possible to select atoms by element?
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Irfan Alibay 已转推
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 mdanalysis.org/2023/02/22/gso…
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Link to the poster if you don't happen to be at #bps2023 github.com/IAlibay/MDAnal…
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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" -> github.com/MDAnalysis/MDA… 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!
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@jandom_random @ExplainedByCats Much worse UX, but probably much better validation? ;)
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@ExplainedByCats @HighSpeedMode App store for MDA? nice play!!
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Last year, @MDAnlaysis released a whitepaper outlining our proposed "MDAKits" -> github.com/MDAnalysis/MDA…
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!
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@Dummyinresearch @ExplainedByCats @mdanalysis @lilyminium @orbeckst We do have a contribution guide in our user documentation: userguide.mdanalysis.org/stable/contrib…
We always welcome any additions/comments/suggestions on how we can improve. Please do open up an issue: github.com/MDAnalysis/Use…
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@ExplainedByCats @mdanalysis @HighSpeedMode @lilyminium @orbeckst MdAnalysis developers should write a tutorial on how to contribute to MDAnalysis for beginner. Much needed.
Python and GitHub is easy to implement, with chatgpt and stack overflow, but main bottleneck is where to start.
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Irfan Alibay 已转推
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 !
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@mia_rosenfeld @ExplainedByCats @mdanalysis @lilyminium @orbeckst That sounds awesome, we're in 6A this morning if you want to trade!
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@ExplainedByCats @mdanalysis @HighSpeedMode @lilyminium @orbeckst OMGGGGGGGG I NEED ONE OF THESE FOR MY HYDROFLASK!!!!!!! 😍 i’ll trade you a pride progress flag pin for your name badge lanyard?!!!!!
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@ExplainedByCats @mdanalysis @lilyminium @orbeckst Come see us at the @mdanalysis poster on Tuesday! Hall BC B446 @ 13:45
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