Jakub Rydzewski

Nicolaus Copernicus University — Poland

Biochemistry, Genetics and Molecular Biology · Life Sciences

12h-index1.6kcitations52works3.12yr avg
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Research Topics

Protein Structure and Dynamics(15), Spectroscopy and Quantum Chemical Studies(8), Machine Learning in Materials Science(8), Neural dynamics and brain function(6), Photoreceptor and optogenetics research(6)

Publications52 total

Decoding dissociation pathways of ligands in prolyl oligopeptidase
Physical Chemistry Chemical Physics·2025
Constructing Generalized Sample Transition Probabilities with Biased Simulations
Journal of Chemical Theory and Computation·2025
<tt>NeuralTSNE</tt>: A Python Package for the Dimensionality Reduction of Molecular Dynamics Data Using Neural Networks
Journal of Chemical Information and Modeling·2025· 1 citedOpen Access
NeuralTSNE: A Python Package for the Dimensionality Reduction of Molecular Dynamics Data Using Neural Networks
arXiv (Cornell University)·2025Open Access
Illuminating Protein Dynamics: A Review of Computational Methods for Studying Photoactive Proteins
arXiv (Cornell University)·2025Open Access
Decoding Binding Pathways of Ligands in Prolyl Oligopeptidase
arXiv (Cornell University)·2025Open Access
PLUMED Tutorials: A collaborative, community-driven learning ecosystem
The Journal of Chemical Physics·2025· 24 citedOpen Access
Machine Learning of Slow Collective Variables and Enhanced Sampling via Spatial Techniques
2025Open Access
Cytochrome P450 inhibition impedes pyrethroid effects on insects through Nav channel regulation
2025Open Access
Machine learning of slow collective variables and enhanced sampling via spatial techniques
Chemical Physics Reviews·2025· 11 citedOpen Access
BPS2025 - Decoding entrance paths for ligands to prolyl oligopeptidase
Biophysical Journal·2025
Machine Learning of Slow Collective Variables and Enhanced Sampling via Spatial Techniques
arXiv (Cornell University)·2024Open Access
Correction to “Spectral Map: Embedding Slow Kinetics in Collective Variables”
The Journal of Physical Chemistry Letters·2024Open Access
A Note on Spectral Map
arXiv (Cornell University)·2024Open Access
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Research Portal (Queen's University Belfast)·2024· 2 citedOpen Access
Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles
Journal of Chemical Theory and Computation·2024· 8 citedOpen Access
Structural visualization of inhibitor binding in prolyl oligopeptidase
Biophysics Reviews·2024· 2 citedOpen Access
Learning Markovian dynamics with spectral maps
The Journal of Chemical Physics·2024· 7 cited
Learning Markovian Dynamics with Spectral Maps
arXiv (Cornell University)·2023Open Access
Spectral Maps for Learning Reduced Representations of Molecular Systems
arXiv (Cornell University)·2023Open Access
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Frequent Co-authors

Wiesław Nowak(19), Ómar Valsson(11), Katarzyna Walczewska-Szewc(8), Tuğçe Gökdemir(7), Ming Chen(5), Sylwia Czach(4), Massimiliano Bonomi(3), Giovanni Bussi(3), Carlo Camilloni(3), Gareth A. Tribello(3), Mattia Bernetti(3), Riccardo Capelli(3), Michele Ceriotti(3), Davide Donadio(3), Bernd Ensing(3), Andrew L. Ferguson(3), Francesco Luigi Gervasio(3), Toni Giorgino(3), Glen M. Hocky(3), Michele Invernizzi(3)