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
1802019
Ligand diffusion in proteins via enhanced sampling in molecular dynamics
J Rydzewski, W Nowak
Physics of Life Reviews 22, 58-74, 2017
402017
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
212016
Memetic algorithms for ligand expulsion from protein cavities
J Rydzewski, W Nowak
The Journal of chemical physics 143 (12), 124101, 2015
212015
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
202018
Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations
J Rydzewski, W Nowak
Scientific Reports 7, 7736, 2017
102017
Finding multiple reaction pathways of ligand unbinding
J Rydzewski, O Valsson
The Journal of chemical physics 150 (22), 221101, 2019
92019
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), 171103, 2015
82015
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
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
42021
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
42019
maze: Heterogeneous ligand unbinding along transient protein tunnels
J Rydzewski
Computer Physics Communications 247, 106865, 2020
32020
Photoinduced transport in an H64Q neuroglobin antidote for carbon monoxide poisoning
J Rydzewski, W Nowak
The Journal of chemical physics 148 (11), 115101, 2018
32018
Conformational sampling of a biomolecular rugged energy landscape
J Rydzewski, R Jakubowski, G Nicosia, W Nowak
IEEE/ACM transactions on computational biology and bioinformatics 15 (3 …, 2016
22016
Nanomechanics of PCNA: a protein-made DNA sliding clamp
J Rydzewski, W Strzalka, W Nowak
Chemical Physics Letters 634, 236–242, 2015
22015
Molecular dynamics simulations of large systems in electronic excited states
J Rydzewski, W Nowak
Handbook of Computational Chemistry, 2016
12016
Multiscale Reweighted Stochastic Embedding (MRSE): Deep Learning of Collective Variables for Enhanced Sampling (Version 1.0.0) [Data set].
J Rydzewski, O Valsson
https://doi.org/10.5281/zenodo.4756093, 2021
2021
Non-Equilibrium Processes in Proteins Triggered by Light: Excited States Molecular Dynamics Perspective
J Rydzewski, L Peplowski, K Walczewska-Szewc, P Miszta, ...
European Biophysics Journal with Biophysics Letters 48, S44-S44, 2019
2019
Rare-Event Sampling of Ligand Transport in Proteins
J Rydzewski
Institute of Physics, Nicolaus Copernicus University, 2018
2018
Photoswitchable Drugs and Insulin Release: Molecular Events in the EPAC2A Protein
L Peplowski, J Rydzewski, T Miyahara, H Nakamura, H Nakatsuji, ...
Biophysical Journal 114 (3), 31a, 2018
2018
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