You may find my full academic list on google scholar and ORCID. However, if you want some personal insights about selected papers (in reverse chronological order) – please read along😎

2024

Split-and-combine parallelization for MDAnalysis AnalysisBase subclasses

You can find all about this project by gsoc tag, but basically, you can now do ArbitraryAnalysisSubclass.run(backend='multiprocessing'), and it’ll run automatically in multiple processes.

You can read more about parallelization on docs, especially some limitations of the current approach.

Secondary structure analysis with DSSP for MDAnalysis

A fun project emerged during MDAnalysis 2023 UGM hackathon. Basically, it adds a built-in secondary structure analysis, with no dependencies. The algorithm is based on Kabsch et al, and implementation is borrowed from pyDSSP. I slightly modified the implementation, making it depend only on numpy (previously it depended on einops package).

For details, see documentation.

A subgroup of light-driven sodium pumps with an additional Schiff base counterion

A project led by super talented Kirill Kovalev. Whereas it’s always a pleasure to work with Kirill, it’s also a great study that combines multiple techniques, both functional and structural, to study a novel rhodopsin. For me personally, it’s a first paper that confirms I can do cryoEM data processing🥶

On the methods of studying protein-ligand interaction dynamics

My thesis, written under supervision of Albert Guskov, Valentin Borshchevskiy and Dirk Slotboom. The text is open access, and is basically composed of few articles mentioned below, plus some extra nice acknowledgements in multiple languages.

2023

Regression-Based Active Learning for Accessible Acceleration of Ultra-Large Library Docking

Amazing (conflict of interest: I am the last author) paper, where we basically show that deep learning isn’t needed for accelerated virtual screening.

For more info, please go to the article description

Custom Design of a Humidifier Chamber for In Meso Crystallization

A neat paper that shares an open-source design (as in “to assemble on your own if you have decent skills”) of a humidifier chamber for a Gryphon crystallization robot, that unfortunately doesn’t have such chamber.

Structural insights into the effects of glycerol on ligand binding to cytochrome P450

Neat piece of evidence showing that glycerol (a common cryoprotectant in crystallography) can significantly effect the binding pose, constrain it, and make the conformational ensemble of protein-ligand compless less rich.

2022

Structural basis for receptor selectivity and inverse agonism in S1P5 receptors

Super cool paper, many challenging tasks – patent parsing, docking, serial crystallography, computer vision, etc. For more detail, please read the article description.

2021

Structural aspects of photopharmacology: insight into the binding of photoswitchable and photocaged inhibitors to the glutamate transporter homologue

Photo. Switchable. Ligands. A prospect towards time-resolved studies and other things. Not by me though, I only did docking to confirm relatively unclear binding poses revealed by crystallography.

2020

Structure-Based Virtual Screening of Ultra-Large Library Yields Potent Antagonists for a Lipid GPCR

Large-scale VLS that didn’t work as good as we hoped, but gave (at least me) a good perspective on such studies.

Small-wedge synchrotron and serial XFEL datasets for Cysteinyl leukotriene GPCRs

Huge dataset with serial crystallography data across wide range of resolutions and techniques.

Molecular mechanism of light-driven sodium pumping

Very cool study that shows a serial crystallography (with a jet!) dataset collected at ALBA synchrotron. The structure itself reveals a “trapped” state of KR2 rhodopsin.

2019

Structural basis of ligand selectivity and disease mutations in cysteinyl leukotriene receptors

CysLT2 paper, with lots of docking and crystallography.

Structure-based mechanism of cysteinyl leukotriene receptor inhibition by antiasthmatic drugs

CysLT1 paper, with lots of molecular dynamics, functional tests, and hopes.

2017

Structural insights into ion conduction by channelrhodopsin 2

Very long awaited publication, which was also a very random co-authorship for me, though I’m very grateful for that.

Element-specific density profiles in interacting biomembrane models

My very first publication, written during DESY Summerschool program. I validated someone else’s data processing, and got the same results, confirming that it’s a solid data processing pipeline.