marimo: Python notebooks that are just Python post

What marimo is, why I like it, and a live notebook running right in this page

Split-and-combine parallelization for MDAnalysis AnalysisBase subclasses post

Parallel AnalysisBase.run() in MDAnalysis with multiprocessing and dask: the outcome of my GSoC 2023 project

Secondary structure analysis with DSSP for MDAnalysis post

Built-in, dependency-free secondary structure analysis (DSSP) for MDAnalysis, started at the 2023 UGM hackathon

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

Nature Communications, 2024

On the methods of studying protein-ligand interaction dynamics paper

PhD thesis, University of Groningen, 2024

Regression-based Accelerated Virtual Screening post

A lesser formal version of this JCIM paper

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

Journal of Chemical Information and Modeling, 2023

Custom Design of a Humidifier Chamber for In Meso Crystallization paper

Crystal Growth & Design, 2023

MDAnalysis UGM 2023: MDAnalysis Parallelization @ GSOC post

Presentation given at the MDAnalysis User Meeting in 2023

Taskfile + uv for running python tests til

A quick note on how to write a Taskfile to make running tests easies

GSOC-2023: summary post

Summary of the GSOC work on MDAnalysis parallelization

(again bi)weekly GSOC-4: finally about results aggretation post

Fourth biweekly GSOC blogpost

(not anymore bi)weekly GSOC-3: writing `ParallelExecutor` class post

Third biweekly GSOC blogpost

Biweekly GSOC-2: splitting the work and writing `_setup_bslices` post

Second biweekly GSOC blogpost

Biweekly GSOC-1: decomposing `AnalysisBase.run()` post

First biweekly GSOC blogpost

GSOC 2023: what will I do? post

A project proposal, written for GSOC-2023 at MDAnalysis

Fast hex to np.ndarray til

Short story about transforming chemfp fingerprint representation into numpy ndarray

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

Acta Crystallographica Section D Structural Biology, 2023

Structural basis for receptor selectivity and inverse agonism in S1P5 receptors post

A lesser formal version of this Nature Communications paper

Structural basis for receptor selectivity and inverse agonism in S1P5 receptors paper

Nature Communications, 2022

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

Journal of the American Chemical Society, 2021

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

Biomolecules, 2020

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

Scientific Data, 2020

Molecular mechanism of light-driven sodium pumping paper

Nature Communications, 2020

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

Nature Communications, 2019

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

Science Advances, 2019

Structural insights into ion conduction by channelrhodopsin 2 paper

Science, 2017

Element-specific density profiles in interacting biomembrane models paper

Journal of Physics D: Applied Physics, 2017