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 | 424 | 2019 |
Promoting transparency and reproducibility in enhanced molecular simulations Nature methods 16 (8), 670-673, 2019 | 229 | 2019 |
Ligand diffusion in proteins via enhanced sampling in molecular dynamics J Rydzewski, W Nowak Physics of Life Reviews 22, 58-74, 2017 | 57 | 2017 |
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 | 37 | 2016 |
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 | 31 | 2018 |
Finding multiple reaction pathways of ligand unbinding J Rydzewski, O Valsson The Journal of Chemical Physics 150 (22), 2019 | 28 | 2019 |
Memetic algorithms for ligand expulsion from protein cavities J Rydzewski, W Nowak The Journal of chemical physics 143 (12), 124101, 2015 | 25 | 2015 |
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 | 24 | 2021 |
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 | 16 | 2015 |
Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations J Rydzewski, W Nowak Scientific Reports 7, 7736, 2017 | 13 | 2017 |
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 | 10 | 2022 |
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 | 10 | 2019 |
Manifold Learning in Atomistic Simulations: A Conceptual Review J Rydzewski, M Chen, O Valsson Machine Learning: Science and Technology 4 (3), 031001, 2023 | 9 | 2023 |
maze: Heterogeneous ligand unbinding along transient protein tunnels J Rydzewski Computer Physics Communications 247, 106865, 2020 | 8 | 2020 |
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 | 7 | 2019 |
Photoinduced transport in an H64Q neuroglobin antidote for carbon monoxide poisoning J Rydzewski, W Nowak The Journal of Chemical Physics 148 (11), 2018 | 7 | 2018 |
Spectral map: Embedding slow kinetics in collective variables J Rydzewski The Journal of Physical Chemistry Letters 14 (22), 5216-5220, 2023 | 5 | 2023 |
Selecting high-dimensional representations of physical systems by reweighted diffusion maps J Rydzewski The Journal of Physical Chemistry Letters 14 (11), 2778-2783, 2023 | 5 | 2023 |
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 | 5 | 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 | 5 | 2022 |