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Jakub Rydzewski
Jakub Rydzewski
Institute of Physics, Nicolaus Copernicus University
Verified email at fizyka.umk.pl - Homepage
Title
Cited by
Cited by
Year
Promoting transparency and reproducibility in enhanced molecular simulations
M Bonomi, G Bussi, C Camilloni, GA Tribello, P Banáš, A Barducci, ...
Nature methods 16 (8), 670-673, 2019
4142019
Promoting transparency and reproducibility in enhanced molecular simulations
Nature methods 16 (8), 670-673, 2019
2202019
Ligand diffusion in proteins via enhanced sampling in molecular dynamics
J Rydzewski, W Nowak
Physics of Life Reviews 22, 58-74, 2017
572017
Machine learning based dimensionality reduction facilitates ligand diffusion paths assessment: a case of cytochrome P450cam
J Rydzewski, W Nowak
Journal of Chemical Theory and Computation 12, 2110 − 2120, 2016
372016
Kinetics of huperzine A dissociation from acetylcholinesterase via multiple unbinding pathways
J Rydzewski, R Jakubowski, W Nowak, H Grubmuller
Journal of Chemical Theory and Computation 14 (6), 2843-2851, 2018
312018
Finding multiple reaction pathways of ligand unbinding
J Rydzewski, O Valsson
The Journal of Chemical Physics 150 (22), 2019
272019
Memetic algorithms for ligand expulsion from protein cavities
J Rydzewski, W Nowak
The Journal of chemical physics 143 (12), 124101, 2015
252015
Multiscale reweighted stochastic embedding: Deep learning of collective variables for enhanced sampling
J Rydzewski, O Valsson
The Journal of Physical Chemistry A 125 (28), 6286-6302, 2021
242021
Communication: Entropic measure to prevent energy over-minimization in molecular dynamics simulations
J Rydzewski, R Jakubowski, W Nowak
The Journal of Chemical Physics 143 (17), 2015
162015
Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations
J Rydzewski, W Nowak
Scientific Reports 7, 7736, 2017
132017
Reweighted manifold learning of collective variables from enhanced sampling simulations
J Rydzewski, M Chen, TK Ghosh, O Valsson
Journal of Chemical Theory and Computation 18 (12), 7179-7192, 2022
102022
Manifold Learning in Atomistic Simulations: A Conceptual Review
J Rydzewski, M Chen, O Valsson
Machine Learning: Science and Technology 4 (3), 031001, 2023
92023
A community effort to promote transparency and reproducibility in enhanced molecular simulations
G Bussi, C Camilloni, G Tribello, P Banáš, M Bernetti, PG Bolhuis, ...
Nat. Methods 16, 667-673, 2019
92019
maze: Heterogeneous ligand unbinding along transient protein tunnels
J Rydzewski
Computer Physics Communications 247, 106865, 2020
82020
Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations
JF Carrascoza Mayén, J Rydzewski, N Szostak, J Blazewicz, W Nowak
Life 9 (2), 46, 2019
72019
Photoinduced transport in an H64Q neuroglobin antidote for carbon monoxide poisoning
J Rydzewski, W Nowak
The Journal of Chemical Physics 148 (11), 2018
72018
Spectral map: Embedding slow kinetics in collective variables
J Rydzewski
The Journal of Physical Chemistry Letters 14 (22), 5216-5220, 2023
52023
Selecting high-dimensional representations of physical systems by reweighted diffusion maps
J Rydzewski
The Journal of Physical Chemistry Letters 14 (11), 2778-2783, 2023
52023
Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome
J Rydzewski, K Walczewska-Szewc, S Czach, W Nowak, K Kuczera
Journal of Physical Chemistry B 126 (14), 2647–2657, 2022
52022
Rare-event sampling in ligand diffusion: Reply to comments on" Ligand diffusion in proteins via enhanced sampling in molecular dynamics"
J Rydzewski, W Nowak
Physics of Life Reviews 22, 85-87, 2017
52017
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