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Jakub Rydzewski
Jakub Rydzewski
Institute of Physics, Nicolaus Copernicus University
Zweryfikowany adres z fizyka.umk.pl - Strona główna
Tytuł
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Cytowane przez
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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
2902019
Ligand diffusion in proteins via enhanced sampling in molecular dynamics
J Rydzewski, W Nowak
Physics of Life Reviews 22, 58-74, 2017
422017
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
252016
Memetic algorithms for ligand expulsion from protein cavities
J Rydzewski, W Nowak
The Journal of chemical physics 143 (12), 124101, 2015
242015
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
232018
Finding multiple reaction pathways of ligand unbinding
J Rydzewski, O Valsson
The Journal of Chemical Physics 150 (22), 221101, 2019
142019
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
122015
Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations
J Rydzewski, W Nowak
Scientific Reports 7, 7736, 2017
112017
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
72021
Photoinduced transport in an H64Q neuroglobin antidote for carbon monoxide poisoning
J Rydzewski, W Nowak
The Journal of Chemical Physics 148 (11), 115101, 2018
62018
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
62017
maze: Heterogeneous ligand unbinding along transient protein tunnels
J Rydzewski
Computer Physics Communications 247, 106865, 2020
52020
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
Nanomechanics of PCNA: a protein-made DNA sliding clamp
J Rydzewski, W Strzalka, W Nowak
Chemical Physics Letters 634, 236–242, 2015
32015
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
Molecular dynamics simulations of large systems in electronic excited states
J Rydzewski, W Nowak
Handbook of Computational Chemistry, 2016
12016
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
2022
Inhibition-mediated changes in prolyl oligopeptidase dynamics possibly related to α-synuclein aggregation
K Walczewska-Szewc, J Rydzewski, A Lewkowicz
Physical Chemistry Chemical Physics 24, 4366-4373, 2022
2022
Learning Stochastic Representations of Physical Systems
J Rydzewski, O Valsson
2021
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
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