Oliver Beckstein [he/him]

Shivan Dragon (I was so excited when I pulled it from an Unlimited Starter ... I still play it when I play dragons)

MDAnalysis User Group Meeting (logo)

Come to the @mdanalysis.bsky.social User Group Meeting at Arizona State University in November. See www.mdanalysis.org/2025/07/15/u... for our keynote speakers and more updates.

Great opportunity for junior researchers to present their work and to network with the MDAnalysis community.

Bayesian Nonparametric Analysis of Residence Times for Protein–Lipid Interactions in Molecular Dynamics Simulations Molecular Dynamics (MD) simulations are a versatile tool to investigate the interactions of proteins within their environments, in particular, of membrane proteins with the surrounding lipids. However, quantitative analysis of lipid–protein binding kinetics has remained challenging due to considerable noise and low frequency of long binding events, even in hundreds of microseconds of simulation data. Here, we apply Bayesian nonparametrics to compute residue-resolved residence time distributions from MD trajectories. Such an analysis characterizes binding processes at different time scales (quantified by their kinetic off-rate) and assigns to each trajectory frame a probability of belonging to a specific process. In this way, we classify trajectory frames in an unsupervised manner and obtain, for example, different binding poses or molecular densities based on the time scale of the process. We demonstrate our approach by characterizing interactions of cholesterol with six different G-protein-coupled receptors (A2AAR, β2AR, CB1R, CB2R, CCK1R, and CCK2R) simulated with coarse-grained MD simulations with the MARTINI model. The nonparametric Bayesian analysis allows us to connect the coarse binding time series data to the underlying molecular picture and thus not only infers accurate binding kinetics with error distributions from MD simulations but also describes molecular events responsible for the broad range of kinetic rates.

Ricky Sexton (in collaboration with Mohamadreza Fazel, Maxwell Schweiger and Steve Pressé at ASU) devised a Bayesian nonparametric analysis to robustly and accurately protein-lipid interactions (residence times) from MD simulations – see doi.org/10.1021/acs.... .

KLAXON 🚨: Indie SAGE has come out of retirement to release a new short report standing up for diversity, equity and inclusion (DEI) in the sciences!

DEI is not just the right thing to do, it *improves* the quality of the science. Please read and share.

independentsage.org/wp-content/u...

1/2

You literally cannot tell this incredibly cool part of American history without centering Native American identity. It is an powerful demonstration of how diversity provided tangible military advantages over an enemy committed to White supremacy.
donmoynihan.substack.com/p/whitewashi...

MDAnalysis 2.9.0 (and its blog post) is out: www.mdanalysis.org/2025/03/11/r...!

Includes:
* Additional Gromacs/distopia/parallel analysis support
* New "water"/"precision" keywords

🙏 to the release's 10 contributors (3 new), and to @numfocus.bsky.social/@chanzuckerberg.bsky.social for support.

@biophysicalsoc.bsky.social you need to be sharing at the conference this week like our lives depend on it. Because they do.

Speak up. Stand up. Get out there and protect out democracy

There are three ways to ultimate success:
The first way is to be kind.
The second way is to be kind.
The third way is to be kind
-Fred Rogers

Just shut down for good my twitter account. Live's too short to keep social media accounts that have outlived their time.

Visualization of part of a protein with MDAnalysis and Blender/MolecularNodes together with Python code to generate the image.

🎉 Small Development Grant by @numfocus.bsky.social for Advanced Molecular Visualizations with #MolecularNodes and @blender3d.bsky.social! @yuxuanzhuang.bsky.social and @bradyajohnston.bsky.social will build an API & integrate with @projectjupyter.bsky.social. See www.mdanalysis.org/2024/12/12/s...

I had a hard time finding women physicists here. So I made a starter pack for #female and #under-represended #minorities in #physics, in short #FURMIP.
Please spread the word and
let me know if you would like to be added.
go.bsky.app/2JeYsDz

A reminder that the most productive science is done in collaborations

Goatcounter www.goatcounter.com seems to be doing a decent job for us at mdanalysis.goatcounter.com

Very pleased that our MDverse project was awarded a prize for Open Science

How to get answers in a public forum · MDAnalysis mdanalysis · Discussion #4558 When I am asking a question in a public forum such as the MDAnalysis Discussions and Discord, I am hoping that someone will take the time to read my question, understand what my problem is, think o...

It's a great essay and top of the "recommended reading list" in a pinned post in the @mdanalysis.bsky.social forum to help people getting answers github.com/MDAnalysis/m...

I'm fuming about another email chain with someone asking me for help with some scientific software I support, so I suppose it's a good time to repost this essay I wrote about how to be a good member of a software community:

livecomsjournal.org/index.php/li...

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.

📢📢 Registration for #mdaUGM2024 is now open! Join us in London from 21-23 Aug to talk about all things MDAnalysis. You also won't want to miss the talks from our keynote speakers, Drs. Antonia Mey and Francesca Stanzione.

Register now to secure your place:
www.mdanalysis.org/pages/ugm202...

MDAnalysis Workshop June 24-25th 2024, Arizona State University. Stylized saguaro cactus with flowers shaped like the MDAnalysis logo.

Register for our joint MDAnalysis/MolSSI workshop at Arizona State University on June 24th-25th 2024. Attendance is free, travel bursaries are available, register for in-person or online attendance at www.mdanalysis.org/2024/05/14/A... Registration deadline is soon, May 27, 2024.

MDAnalysis Workshop June 24-25th 2024 at Arizona State University. A Saguaro cactus in the desert with flowers shaped like the MDAnalysis logo.

Save the date: June 24th & 25th: Joint MDAnalysis/MolSSI workshop at Arizona State University. Details to follow.

www.mdanalysis.org/2024/04/24/A...

Submit your abstract to present at the 2024 @mdanalysis.bsky.social User Group Meeting in London. I so look forward to seeing what everybody is up to!

MDAnalysis will be in GSoC 2024! Do you have experience with MD or other simulations, and like coding to solve problems in biophysics/chemistry/materials?

Read our blog on how to apply to work on MDAnalysis: www.mdanalysis.org/2024/02/27/g...

Start early! Pre-proposals are due by March 15th.

Brady Johnston, the author of the structural biology plugin MolecularNodes for blender is one of the instructors: so if you want to learn amazing visualization of your simulations, register. Places will probably be gone soon.

Do you know some Python but want to learn about analyzing and visualizing molecular simulation data? Join us Feb 28 at 3:00 UTC for a free workshop on a basic workflow with MDAnalysis and Molecular Nodes!

Spots are limited, so make sure to apply before Feb 19: www.mdanalysis.org/2024/02/05/m...

P.S.: Attendance is FREE — no conference fees (thanks to a generous EOSS5 grant from the Chan-Zuckerberg Initiative). You just have to apply and register to secure your spot.

P.S.: Attendance is FREE (thanks to funding from the Chan-Zuckerberg Initiative under an EOSS5 grant)— you just have to apply!

Join us for the second MDAnalysis User Group Meeting, this time in London. Submit abstracts! We also have travel bursaries, especially for students/postdocs who would not otherwise be able to attend.

Looking for some good Friday reading? Check out the amazing work Xu Hong and Egor completed during the GSoC 2023 program:

www.mdanalysis.org/2024/01/18/g...

Also, please get in touch with us if you are interested in #mentoring with MDAnalysis for the GSoC 2024 program!

🗓️ Save the date for #mdaUGM2024 ! 🗓️

The MDAnalysis UGM 2024 will take place August 21-23, 2024 in London, UK at King's College London, in partnership with the Thomas Young Centre! Stay tuned for updates.

www.mdanalysis.org/blog/#save-t...

Happy new year to everyone! Enjoy MDAnalysis 2.7.0 www.mdanalysis.org/2024/01/04/r... now with Python 3.12 support, GROMOS11 file format reader, improved nucleic acid analysis, bug fixes and more enhancements. Special thanks to 5 new contributors!