Jakub Rydzewski

According to our database, Jakub Rydzewski authored at least 9 papers between 2018 and 2026.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2026

Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot with Thermodynamics-Driven Machine Learning.

Mariia Ivonina, Jakub Rydzewski

CoRR, April, 2026

2025

<tt>NeuralTSNE</tt>: A Python Package for the Dimensionality Reduction of Molecular Dynamics Data Using Neural Networks.

Patryk Tajs, Mateusz Skarupski, Jakub Rydzewski

J. Chem. Inf. Model., 2025

2024

Machine Learning of Slow Collective Variables and Enhanced Sampling via Spatial Techniques.

Tugçe Gökdemir, Jakub Rydzewski

CoRR, 2024

A Note on Spectral Map.

Tugçe Gökdemir, Jakub Rydzewski

CoRR, 2024

Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles.

Jakub Rydzewski

CoRR, 2024

2023

Manifold learning in atomistic simulations: a conceptual review.

Jakub Rydzewski, Ming Chen, Omar Valsson

Mach. Learn. Sci. Technol., September, 2023

2022

Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations.

Jakub Rydzewski, Ming Chen, Tushar K. Ghosh, Omar Valsson

CoRR, 2022

2020

maze: Heterogeneous ligand unbinding along transient protein tunnels.

Jakub Rydzewski

Comput. Phys. Commun., 2020

2018

Conformational Sampling of a Biomolecular Rugged Energy Landscape.

Jakub Rydzewski, Rafal Jakubowski, Giuseppe Nicosia, Wieslaw Nowak

IEEE ACM Trans. Comput. Biol. Bioinform., 2018