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J

Jakub Rydzewski

physics

13H-index
53Paper Count
1.6KCitation Count
Published Papers 23
Publication Date
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Cytochrome P450 inhibition impedes the insecticide pyrethroid effects on insects through Nav channels regulation
errBMC Biology
IF4.5
err2026-04-29
err0
errOAAI
errBeata Niklas; Eléonore Moreau; Caroline Deshayes; Jakub Rydzewski; Milena Jankowska; Jacek Kęsy; Ademir J. Martins; Pie Müller; Vincent Corbel; Wiesław Nowak; Bruno Lapied
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Decoding Dissociation Pathways of Ligands in Prolyl Oligopeptidase
errPhys. Chem. Chem. Phys.
IF0
err2025-12-09
err0
PREAI
errKatarzyna Walczewska-Szewc; Jakub Rydzewski
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errSave
Constructing Generalized Sample Transition Probabilities with Biased Simulations
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2025-11-01
err0
PREAI
errWang, Yanbin; Rydzewski, Jakub; Chen, Ming
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NeuralTSNE: A Python Package for the Dimensionality Reduction of Molecular Dynamics Data Using Neural Networks
errJournal of Chemical Information and Modeling
IF5.3
err2025-07-14
err0
errOAAI
errPatryk Tajs; Mateusz Skarupski; Jakub Rydzewski
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PLUMED Tutorials: A collaborative, community-driven learning ecosystem
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2025-03-07
err1
PREAI
errTribello, Gareth A.; Bonomi, Massimiliano; Bussi, Giovanni; Camilloni, Carlo; Armstrong, Blake I.; Arsiccio, Andrea; Aureli, Simone; Ballabio, Federico; Bernetti, Mattia; Bonati, Luigi; Brookes, Samuel G. H.; Brotzakis, Z. Faidon; Capelli, Riccardo; Ceriotti, Michele; Chan, Kam-Tung; Cossio, Pilar; Dasetty, Siva; Donadio, Davide; Ensing, Bernd; Ferguson, Andrew L.; Fraux, Guillaume; Gale, Julian D.; Gervasio, Francesco Luigi; Giorgino, Toni; Herringer, Nicholas S. M.; Hocky, Glen M.; Hoff, Samuel E.; Invernizzi, Michele; Languin-Cattoen, Olivier; Leone, Vanessa; Limongelli, Vittorio; Lopez-Acevedo, Olga; Marinelli, Fabrizio; Febrer Martinez, Pedro; Masetti, Matteo; Mehdi, Shams; Michaelides, Angelos; Murtada, Mhd Hussein; Parrinello, Michele; Piaggi, Pablo M.; Pietropaolo, Adriana; Pietrucci, Fabio; Pipolo, Silvio; Pritchard, Claire; Raiteri, Paolo; Raniolo, Stefano; Rapetti, Daniele; Rizzi, Valerio; Rydzewski, Jakub; Salvalaglio, Matteo; Schran, Christoph; Seal, Aniruddha; Shayesteh Zadeh, Armin; Silva, Tomas F. D.; Spiwok, Vojtech; Stirnemann, Guillaume; Sucerquia, Daniel; Tiwary, Pratyush; Valsson, Omar; Vendruscolo, Michele; Voth, Gregory A.; White, Andrew D.; Wu, Jiangbo
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Machine learning of slow collective variables and enhanced sampling via spatial techniques
errCHEMICAL PHYSICS REVIEWS
IF6.2
err2025-02-03
err0
errOAAI
errGokdemir, Tugce; Rydzewski, Jakub
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Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2024-09-12
err1
errOAAI
errRydzewski, Jakub
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errSave
Learning Markovian dynamics with spectral maps
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2024-03-04
err2
errOAAI
errRydzewski, Jakub; Gokdemir, Tugce
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errSave
Manifold learning in atomistic simulations: a conceptual review
errMACHINE LEARNING-SCIENCE AND TECHNOLOGY
IF4.6
err2023-09-05
err9
errOAAI
errRydzewski, Jakub; Chen, Ming; Valsson, Omar
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errSave
Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2022-11-11
err12
errOAAI
errRydzewski, Jakub; Chen, Ming; Ghosh, Tushar K. .; Valsson, Omar
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maze: Heterogeneous ligand unbinding along transient protein tunnels
errCOMPUTER PHYSICS COMMUNICATIONS
IF3.4
err2020-02-01
err11
errOAAI
errRydzewski, Jakub
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errSave
Promoting transparency and reproducibility in enhanced molecular simulations
errNATURE METHODS
IF32.1
err2019-07-30
err715
errOAAI
errBonomi, Massimiliano; Bussi, Giovanni; Camilloni, Carlo; Tribello, Gareth A.; Banas, Pavel; Barducci, Alessandro; Bernetti, Mattia; Bolhuis, Peter G.; Bottaro, Sandro; Branduardi, Davide; Capelli, Riccardo; Carloni, Paolo; Ceriotti, Michele; Cesari, Andrea; Chen, Haochuan; Chen, Wei; Colizzi, Francesco; De, Sandip; De La Pierre, Marco; Donadio, Davide; Drobot, Viktor; Ensing, Bernd; Ferguson, Andrew L.; Filizola, Marta; Fraser, James S.; Fu, Haohao; Gasparotto, Piero; Gervasio, Francesco Luigi; Giberti, Federico; Gil-Ley, Alejandro; Giorgino, Toni; Heller, Gabriella T.; Hocky, Glen M.; Iannuzzi, Marcella; Invernizzi, Michele; Jelfs, Kim E.; Jussupow, Alexander; Kirilin, Evgeny; Laio, Alessandro; Limongelli, Vittorio; Lindorff-Larsen, Kresten; Lohr, Thomas; Marinelli, Fabrizio; Martin-Samos, Layla; Masetti, Matteo; Meyer, Ralf; Michaelides, Angelos; Molteni, Carla; Morishita, Tetsuya; Nava, Marco; Paissoni, Cristina; Papaleo, Elena; Parrinello, Michele; Pfaendtner, Jim; Piaggi, Pablo; Piccini, GiovanniMaria; Pietropaolo, Adriana; Pietrucci, Fabio; Pipolo, Silvio; Provasi, Davide; Quigley, David; Raiteri, Paolo; Raniolo, Stefano; Rydzewski, Jakub; Salvalaglio, Matteo; Sosso, Gabriele Cesare; Spiwok, Vojtech; Sponer, Jiri; Swenson, David W. H.; Tiwary, Pratyush; Valsson, Omar; Vendruscolo, Michele; Voth, Gregory A.; White, Andrew
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errSave
Finding multiple reaction pathways of ligand unbinding
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2019-06-14
err28
errOAAI
errRydzewski, Jakub; Valsson, Omar
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errSave
Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations
errLIFE-BASEL
IF3.4
err2019-06-04
err7
errOAAI
errMayen, Juan Francisco Carrascoza; Rydzewski, Jakub; Szostak, Natalia; Blazewicz, Jacek; Nowak, Wieslaw
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Conformational Sampling of a Biomolecular Rugged Energy Landscape
errIEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
IF3.4
err2018-05-01
err2
PREAI
errRydzewski, Jakub; Jakubowski, Rafal; Nicosia, Giuseppe; Nowak, Wieslaw
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Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2018-05-01
err23
errOAAI
errRydzewski, J.; Jakubowski, R.; Nowak, W.; Grubmueller, H.
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errSave
Photoinduced transport in an H64Q neuroglobin antidote for carbon monoxide poisoning
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2018-03-16
err7
PREAI
errRydzewski, J.; Nowak, W.
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errSave
Photoswitchable Drugs and Insulin Release: Molecular Events in EPAC2A Protein
errBIOPHYSICAL JOURNAL
IF3.1
err2018-02-01
err0
errOAAI
errNowak, Wieslaw A.; Peplowski, Lukasz; Rydzewski, Jakub; Miyahara, Tomoo; Nakamura, Haruki; Nakatsuji, Hiroshi
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Ligand diffusion in proteins via enhanced sampling in molecular dynamics
errPHYSICS OF LIFE REVIEWS
IF14.3
err2017-12-01
err50
PREAI
errRydzewski, J.; Nowak, W.
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errSave
Rare-event sampling in ligand diffusion Reply to comments on Ligand diffusion in proteins via enhanced sampling in molecular dynamics
errPHYSICS OF LIFE REVIEWS
IF14.3
err2017-12-01
err4
PREAI
errRydzewski, J.; Nowak, W.
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errSave

Research Directions

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Co-authors
Cooperation Journals
M
Michele Parrinello
H-index: 155 · Papers: 924
M
Michele Vendruscolo
H-index: 118 · Papers: 1.1K
G
Gregory A. Voth
H-index: 114 · Papers: 985
J
Jiřı́ Šponer
H-index: 87 · Papers: 641
A
Angelos Michaelides
H-index: 84 · Papers: 399
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