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OpenAlex Citation Counts

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OpenAlex is a bibliographic catalogue of scientific papers, authors and institutions accessible in open access mode, named after the Library of Alexandria. It's citation coverage is excellent and I hope you will find utility in this listing of citing articles!

If you click the article title, you'll navigate to the article, as listed in CrossRef. If you click the Open Access links, you'll navigate to the "best Open Access location". Clicking the citation count will open this listing for that article. Lastly at the bottom of the page, you'll find basic pagination options.

Requested Article:

Deeptime: a Python library for machine learning dynamical models from time series data
Moritz Hoffmann, Martin K. Scherer, Tim Hempel, et al.
Machine Learning Science and Technology (2021) Vol. 3, Iss. 1, pp. 015009-015009
Open Access | Times Cited: 82

Showing 1-25 of 82 citing articles:

Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics
Marloes Arts, Víctor García Satorras, Chin‐Wei Huang, et al.
Journal of Chemical Theory and Computation (2023) Vol. 19, Iss. 18, pp. 6151-6159
Open Access | Times Cited: 42
Machine learning heralding a new development phase in molecular dynamics simulations
Eva Prašnikar, Martin Ljubič, Andrej Perdih, et al.
Artificial Intelligence Review (2024) Vol. 57, Iss. 4
Open Access | Times Cited: 20
Protein dynamics underlying allosteric regulation
Miro A. Astore, Akshada S. Pradhan, Erik H. Thiede, et al.
Current Opinion in Structural Biology (2024) Vol. 84, pp. 102768-102768
Open Access | Times Cited: 19
Extreme genome scrambling in marine planktonicOikopleura dioicacryptic species
Charles Plessy, Michael J. Mansfield, Aleksandra Bliznina, et al.
Genome Research (2024)
Open Access | Times Cited: 17
Driving and characterizing nucleation of urea and glycine polymorphs in water
Ziyue Zou, Eric R. Beyerle, Sun-Ting Tsai, et al.
Proceedings of the National Academy of Sciences (2023) Vol. 120, Iss. 7
Open Access | Times Cited: 30
Information Bottleneck Approach for Markov Model Construction
Dedi Wang, Yunrui Qiu, Eric R. Beyerle, et al.
Journal of Chemical Theory and Computation (2024) Vol. 20, Iss. 12, pp. 5352-5367
Open Access | Times Cited: 10
Machine Learning in Soft Matter: From Simulations to Experiments
Kaihua Zhang, Xiangrui Gong, Ying Jiang
Advanced Functional Materials (2024) Vol. 34, Iss. 24
Closed Access | Times Cited: 8
GraphVAMPNet, using graph neural networks and variational approach to Markov processes for dynamical modeling of biomolecules
Mahdi Ghorbani, Samarjeet Prasad, Jeffery B. Klauda, et al.
The Journal of Chemical Physics (2022) Vol. 156, Iss. 18
Open Access | Times Cited: 35
Active Learning of the Conformational Ensemble of Proteins Using Maximum Entropy VAMPNets
Diego E. Kleiman, Diwakar Shukla
Journal of Chemical Theory and Computation (2023) Vol. 19, Iss. 14, pp. 4377-4388
Open Access | Times Cited: 20
Overcoming the timescale barrier in molecular dynamics: Transfer operators, variational principles and machine learning
Christof Schütte, Stefan Klus, Carsten Hartmann
Acta Numerica (2023) Vol. 32, pp. 517-673
Open Access | Times Cited: 18
Thermodynamics-inspired explanations of artificial intelligence
Shams Mehdi, Pratyush Tiwary
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 7
Reaction coordinate flows for model reduction of molecular kinetics
Hao Wu, Frank Noé
The Journal of Chemical Physics (2024) Vol. 160, Iss. 4
Open Access | Times Cited: 6
PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model
Louis G. Smith, Borna Novak, Meghan Osato, et al.
Journal of Chemical Theory and Computation (2024) Vol. 20, Iss. 3, pp. 1036-1050
Open Access | Times Cited: 6
PyKoopman: A Python Package for Data-Driven Approximation of the Koopman Operator
Shaowu Pan, Eurika Kaiser, Brian M. de Silva, et al.
The Journal of Open Source Software (2024) Vol. 9, Iss. 94, pp. 5881-5881
Open Access | Times Cited: 5
A variational approach to assess reaction coordinates for two-step crystallization
Aaron R. Finney, Matteo Salvalaglio
The Journal of Chemical Physics (2023) Vol. 158, Iss. 9
Open Access | Times Cited: 15
Product release and substrate entry of aldehyde deformylating oxygenase revealed by molecular dynamics simulations
Masataka YOSHIMURA, Munehito Arai
Biophysics and Physicobiology (2025) Vol. 22, Iss. 1, pp. n/a-n/a
Open Access
Unveiling G-Protein-Coupled Receptor Conformational Dynamics via Metadynamics Simulations and Markov State Models
Rita Roessner, Nicolas Floquet, Maxime Louet
bioRxiv (Cold Spring Harbor Laboratory) (2025)
Open Access
Markov State Models with Weighted Ensemble Simulation: How to Eliminate the Trajectory Merging Bias
Samik Bose, Ceren Kılınç, Alex Dickson
Journal of Chemical Theory and Computation (2025)
Open Access
Hidden complexity of α7 nicotinic acetylcholine receptor desensitization revealed by MD simulations and Markov state modeling
Mariia Avstrikova, Paula Milán Rodríguez, Sean M. Burke, et al.
Proceedings of the National Academy of Sciences (2025) Vol. 122, Iss. 7
Open Access
Illuminating an invisible state of the HIV-1 capsid protein CTD dimer using 19 F NMR and weighted ensemble simulations
Darian T. Yang, Lillian T. Chong, Angela M. Gronenborn
Proceedings of the National Academy of Sciences (2025) Vol. 122, Iss. 8
Open Access
Leptin Knockdown in Human Adipose Progenitor Cells Alters Adipocyte Function
Lior Fuchs, Donovan Duc, Linnaeus Bundalian, et al.
(2025)
Closed Access
Unsupervised Learning of Progress Coordinates during Weighted Ensemble Simulations: Application to NTL9 Protein Folding
Jeremy M. G. Leung, Nicolas C. Frazee, Alexander Brace, et al.
Journal of Chemical Theory and Computation (2025)
Open Access
EnGens: a computational framework for generation and analysis of representative protein conformational ensembles
Anja Conev, Maurício Rigo, Didier Devaurs, et al.
Briefings in Bioinformatics (2023) Vol. 24, Iss. 4
Open Access | Times Cited: 12
sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data
Joseph Ng, Guillem Montamat, Alexander T. Stewart, et al.
Nature Methods (2023) Vol. 21, Iss. 5, pp. 823-834
Open Access | Times Cited: 12
Stochastic Approximation to MBAR and TRAM: Batchwise Free Energy Estimation
Maaike M. Galama, Hao Wu, Andreas Krämer, et al.
Journal of Chemical Theory and Computation (2023) Vol. 19, Iss. 3, pp. 758-766
Open Access | Times Cited: 11
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