Memory dependent PAth Sampling methods for understanding long TIMEscale molecular processes

Project Information

PASTIME

Grant agreement ID: 101086145

DOI

10.3030/101086145

EC signature date 17 March 2023

Start date 1 September 2023

End date 31 August 2028

Funded under

• European Research Council (ERC)

Total cost

€ 2 000 000,00

EU contribution

€ 2 000 000,00

Coordinated by

UNIVERSITEIT GENT
Belgium

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Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (13)

Conformational dynamics of α‐1 acid glycoprotein (AGP) in cancer: A comparative study of glycosylated and unglycosylated AGP

Author(s): Bhawna Dixit, Wim Vranken, An Ghysels
Published in: Proteins: Structure, Function, and Bioinformatics, Issue 92, 2024, ISSN 0887-3585
Publisher: Wiley
DOI: 10.1002/PROT.26607

PyRETIS 3: Conquering rare and slow events without boundaries

Author(s): Wouter Vervust, Daniel T. Zhang, An Ghysels, Sander Roet, Titus S. van Erp, Enrico Riccardi
Published in: Journal of Computational Chemistry, Issue 45, 2024, ISSN 0192-8651
Publisher: Wiley
DOI: 10.1002/JCC.27319

Journal of Computational Chemistry

Author(s): Wouter Vervust; Daniel T. Zhang; An Ghysels; Sander Roet; Titus S. van Erp; Enrico Riccardi
Published in: Journal of Computational Chemistry, 2024, ISSN 0192-8651
Publisher: Wiley
DOI: 10.1002/JCC.27319

Validation of a Coarse-Grained Martini 3 Model for Molecular Oxygen

Author(s): Samaneh Davoudi, Petteri A. Vainikka, Siewert J. Marrink, An Ghysels
Published in: Journal of Chemical Theory and Computation, Issue 21, 2025, ISSN 1549-9618
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCTC.4C01348

Enhanced molecular docking: Novel algorithm for identifying highest weight k-cliques in weighted general and protein-ligand graphs

Author(s): Kati Rozman, An Ghysels, Bogdan Zavalnij, Tanja Kunej, Urban Bren, Dušanka Janežič, Janez Konc
Published in: Journal of Molecular Structure, Issue 1304, 2024, ISSN 0022-2860
Publisher: Elsevier BV
DOI: 10.1016/J.MOLSTRUC.2024.137639

Proceedings of the National Academy of Sciences of the United States of America

Author(s): Wouter Vervust; Sina Safaei; Katja Witschas; Luc Leybaert; An Ghysels
Published in: Proceedings of the National Academy of Sciences, 2025, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/PNAS.2422437122

Exact Kinetics of Drug Permeation Using Transition Interface Sampling

Author(s): Sina Safaei, Lukas Baldauf, Titus S. van Erp, An Ghysels
Published in: The Journal of Physical Chemistry B, Issue 129, 2025, ISSN 1520-6106
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.JPCB.5C05025

Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics

Author(s): Jose Gavalda-Garcia, Bhawna Dixit, Adrián Díaz, An Ghysels, Wim Vranken
Published in: Journal of Molecular Biology, Issue 437, 2025, ISSN 0022-2836
Publisher: Elsevier BV
DOI: 10.1016/J.JMB.2024.168900

Myelin sheaths can act as compact temporary oxygen storage units as modeled by an electrical RC circuit model

Author(s): Wouter Vervust, Sina Safaei, Katja Witschas, Luc Leybaert, An Ghysels
Published in: Proceedings of the National Academy of Sciences, Issue 122, 2025, ISSN 0027-8424
Publisher: Proceedings of the National Academy of Sciences
DOI: 10.21203/RS.3.RS-4773524/V1

An exact algorithm to find a maximum weight clique in a weighted undirected graph

Author(s): Kati Rozman, An Ghysels, Dušanka Janežič, Janez Konc
Published in: Scientific Reports, Issue 14, 2024, ISSN 2045-2322
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41598-024-59689-X

Capric Acid and Myristic Acid Permeability Enhancers in Curved Liposome Membranes

Author(s): Samaneh Davoudi, Koen Raemdonck, Kevin Braeckmans, An Ghysels
Published in: Journal of Chemical Information and Modeling, Issue 63, 2023, ISSN 1549-9596
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCIM.3C00936

Journal of Chemical Theory and Computation

Author(s): Samaneh Davoudi; Petteri A. Vainikka; Siewert J. Marrink; An Ghysels
Published in: Journal of Chemical Theory and Computation, 2024, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/ACS.JCTC.4C01348

Journal of Chemical Theory and Computation

Author(s): Samaneh Davoudi; Koen Raemdonck; Kevin Braeckmans; An Ghysels
Published in: Journal of Chemical Information and Modeling, 2023, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/ACS.JCIM.3C00936