iiinova — where your digital self keeps evolving

Alek Kovalenko @alekkov.bsky.social · 30/09/2026

Quick start a new Molecular Dynamics/Computational Biology project using my cookiecutter template. This template is tailored to my work style, but you can fork and flexibly reorganise it to your liking and needs! github.com/Aleksandr-bi...

github.com

GitHub - Aleksandr-biochem/md_project_cookiecutter: A cookiecutter template for a Molecular Dynamics simulation project

A cookiecutter template for a Molecular Dynamics simulation project - Aleksandr-biochem/md_project_cookiecutter

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Alek Kovalenko @alekkov.bsky.social · 08/08/2026

Been getting progressively annoyed with looking for a QR-code generator whenever I need one for a presentation or a poster. So now I have my own: aleksandr-biochem.github.io/qr_generator/ And you can bookmark and use it too. No cookies, no ads. Just get your code and go on with your day!

aleksandr-biochem.github.io

QR Generator

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Alek Kovalenko @alekkov.bsky.social · 28/07/2026

It looks like we are past the point of strict disclosure of LLM use in academic writing… I just wish so badly that there was at least some sort of “human-written” badge for papers. I so yearn for texts written by humans🥲 let’s glamorise that

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Alek Kovalenko @alekkov.bsky.social · 21/07/2026

I've just rediscovered Galaxy in a new way thanks to this paper: journals.plos.org/ploscompbiol... Even as someone with two qualifications in Bioinformatics, I used to think that Galaxy is mostly useful for sequence-oriented projects. Looks like much have happened since I learned about it.

journals.plos.org

Ten common misconceptions about Galaxy (and why they are wrong!)

Author summary Galaxy is a free, community-built web interface that helps scientists analyse data in a way that’s easy to use, transparent and reproducible. While it is widely used in biology and othe...

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Reposted by Alek Kovalenko

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 07/06/2026

STOP using ipTM for #AlphaFold PPI screens. * Artificially LOW when both full-length proteins have irrelevant, non-binding IDRs/domains. * If one protein is folded & other contains irrelevant IDRs or domains, the score is too HIGH bc of d0. * Use ipSAE or LIS. www.biorxiv.org/content/10.1...

ipSAE vs ipTM for sorting true interactors from non-interactors. ipSAE is better at separating them.

Post from "AF Cache: Efficient Pipeline for Running AlphaFold for High-Throughput Protein-Protein Interaction Prediction". Various scores on p53/mdm2 interaction.

AlphaFOld ipTM score goes up when extra disorder is added to ONE proten. It goes way down when added to both proteins. Example of KRAS with RAF1 RBD.

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Alek Kovalenko @alekkov.bsky.social · 26/05/2026

Talks from #ColabW26 are now up on youtube! I was especially waiting for the recording of the talk by @malvikasharan.bsky.social This one is easily in my top-5 talks I ever attended. Moving, powerful and stimulating youtu.be/sjmRJQL8PoE?...

youtu.be

What We Carry Forward: Research, Community and Sustainability Under Change - Malvika Sharan

YouTube video by Software Sustainability Institute

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Alek Kovalenko @alekkov.bsky.social · 12/05/2026

Have you ever wanted to try Snakemake workflows, but unsure where to start? Or maybe you use Snakemake, but want to interest your colleagues as well? Never heard of Snakemake? You are about to discover something exciting! Take a look at my quick-start tutorial github.com/Aleksandr-bi...

github.com

GitHub - Aleksandr-biochem/snakemake_md_tutorial: A quickstart tutorial on snakemake with sample data

A quickstart tutorial on snakemake with sample data - Aleksandr-biochem/snakemake_md_tutorial

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Alek Kovalenko @alekkov.bsky.social · 11/05/2026

Oh no, I will have to remember 12 characters instead of 4 now…

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Alek Kovalenko @alekkov.bsky.social · 08/05/2026

This is so cool! Efficient sharing of molecular dynamics data is such a lacking element to empower FAIR practices in molecular simulation research

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Alek Kovalenko @alekkov.bsky.social · 06/05/2026

For today’s group meeting I gave a tutorial on workflows and Snakemake for molecular simulations 🙌🏻

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Alek Kovalenko @alekkov.bsky.social · 03/05/2026

With the #ColabW26 I discovered so many cool projects and resources, so I might as well collect some of them in this thread Starting with Air Quality Stripes airqualitystripes.info

airqualitystripes.info

Air Quality Stripes

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Alek Kovalenko @alekkov.bsky.social · 28/04/2026

Kicked off my first SSI Collaboration Workshop as an online participant today! So many stimulating discussions and much food for thought. Stellar job from the organisers. I feel so involved even being so remote in Oxford 🙌🏻 #CollabW26

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Alek Kovalenko @alekkov.bsky.social · 26/04/2026

Having heard updates on this project at many stages from @robbieclark.bsky.social I can say that this is an amazing work. Congratulations to everyone on the team and to Robbie 🎉

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Alek Kovalenko @alekkov.bsky.social · 06/02/2026

The find of the week for me is RustSASA. So fast and easy to use! I had to work around with `rust-python-sasa` instead of using `MDAnalysis`, because I work with coarse-grained systems in MARTINI. But even then, it gave me ~6x speed-up on my analysis🙌 github.com/maxall41/Rus...

github.com

GitHub - maxall41/RustSASA: A Rust library for calculating the SASA for a protein. 5x faster than Freesasa. Based on the Shrake & Rupley algorithm.

A Rust library for calculating the SASA for a protein. 5x faster than Freesasa. Based on the Shrake & Rupley algorithm. - GitHub - maxall41/RustSASA: A Rust library for calculating the SASA fo...

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Alek Kovalenko @alekkov.bsky.social · 12/02/2025

Very exciting to talk at the OxBacNet meeting held at @dunnschool.bsky.social Summarising mine and @sykhalid.bsky.social collaboration with @augustsilale.bsky.social to investigate a new ExbBD motor structure using molecular dynamics (foreshadowing the manuscript in preparation)

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