Physics of Proteins: Design & Prediction

FOCUS · MAR-M71 · ID: 3112437

Presentations

  • Global epistasis from a physical learning perspective

    ORAL

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    Presenters

    • Farshid Mohammad-Rafiee

      Department of Physics and Astronomy, University of Pennsylvania,

    Authors

    • Farshid Mohammad-Rafiee

      Department of Physics and Astronomy, University of Pennsylvania,

    • Mengyi Sun

      Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory

    • Marcelo Guzmán

      University of Pennsylvania

    • Felipe Martins

      University of Pennsylvania

    • David M McCandlish

      Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory

    • Joshua B Plotkin

      Department of Biology, University of Pennsylvania

    • Andrea J Liu

      University of Pennsylvania

    View abstract →

  • Interactive molecular visualization and simulation: examples and challenges with UDock and VTX

    ORAL · Invited

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    Publication: [1] Levieux G, Tiger G, Natkin S, Zagury JF, Montes M. FD169: UDock, the protein docking entertainment system. Faraday Discuss. 2014, 169 (1): 425-441

    [2] Plateau-Holleville C, Guionnière S, Boyer B, Jimenez-Garcia B, Levieux G, Merillou S, Maria M, Montes M. UDock2: Interactive real-time multi-body protein-protein docking software. Bioinformatics, 2023; 39 (10), btad609

    [3] Plateau-Holleville C, Maria M, Merillou S, Montes M. Efficient GPU computation of large protein Solvent-Excluded Surface. IEEE Trans Vis Comput Graph, 2024

    [4] Maria M, Guionnière S, Dacquay N, Plateau–Holleville C, Guillaume V, Larroque V, Lardé J, Mérillou S, Lagarde N, Naimi Y, Piquemal JP, Levieux G, Montes M. VTX: Real-Time High-Performance Molecular Structure and Dynamics Visualization Software. Submitted manuscript

    Presenters

    • Matthieu Montes

      Conservatoire National des Arts et Metiers, Hesam Universite

    Authors

    • Matthieu Montes

      Conservatoire National des Arts et Metiers, Hesam Universite

    View abstract →

  • Mechano-electrical coupling in PIEZO channels revealed from multiscale simulations

    ORAL

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    Publication: 1. Wen C., Luo, Y., Madsen, J., Optimizing coarse-grained models for large-scale membrane protein simulations, bioRxiv doi.org/10.1101/2024.05.13.594009, 2024
    2. Wijerathne T., Bhatt A., Jiang W., Luo Y., Lacroix J., Mammalian PIEZO channels rectify anionic currents, bioRxiv, 2024.08. 23.609388, 2024
    3. Li S., Wu B., Luo Y., Han W., Simulation of functional motion of super large biomolecules with a mixed-resolution model, J. Chem. Theory Comput., 2024
    4. Jiang W., Wijerathne, T., Zhang H., Lin Y., Jo S., Im W., Lacroix J., Luo Y., Structural and thermodynamic framework for PIEZO1 modulation by small molecules, PNAS, 120, e2310933120, 2023
    5. Jiang W., et. al., Lacroix J., Rohacs T., Luo Y., Crowding-induced opening of the mechanosensitive Piezo1 channel in silico. Commun. Biol. 4, 84, 2021
    6. Jiang, W., Ling, Y., Luo, Y., Mechanical properties of anionic asymmetric bilayers from atomistic simulations, J. Chem. Phys., 2021
    7. Botello-Smith W, Zhang H, Ozkan AD, Jiang W, Pham CN, Lacroix J, Luo Y, A molecular Mechanism for the Chemical Activation of the Mechanosensitive Piezo1 Channel, Nat. Commun., DOI: 10.1038/s41467-019-12501-1.

    Presenters

    • Yun L Luo

      Western University of Health Sciences

    Authors

    • Yun L Luo

      Western University of Health Sciences

    • Shu Li

      Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao SAR 999078

    • Wei Han

      Department of Chemistry, Faculty of Science, Hong Kong Baptist University, Hong Kong SAR 999077

    • Aashish Bhatt

      Western University of Health Sciences

    View abstract →

  • Blocking and single-point mutations of aminoacids in biological enzymes through Protein Residue Networks (PRN) and graph-theory representations. Analysis of local and non-local spreading effects.

    ORAL

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    Publication: 1. AGUILAR PINEDA GE and OLIVARES QUIROZ L. Phys Biol, 18, 066002, (2021). DOI: 10.1088/1478-3975/ac211b.
    2. OLIVARES QUIROZ L. Journal of Complex Networks, Volume 12, Issue 4, August 2024, cnae033, https://doi.org/10.1093/comnet/cnae033
    3. José A Vélez-Pérez and L Olivares-Quiroz 2024 Phys. Scr. 99 1059c8. DOI 10.1088/1402-4896/ad7a2d

    Presenters

    • Luis Olivares-Quiroz

      Universidad Autónoma de la Ciudad de México UACM

    Authors

    • Luis Olivares-Quiroz

      Universidad Autónoma de la Ciudad de México UACM

    • Ohtli Quiroz-Sánchez

      CINVESTAV

    View abstract →

  • Elucidating the Dynamic Interactions of Borrelia burgdorferi Surface Proteins with Fibronectin using Atomic Force Microscopy

    ORAL

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    Presenters

    • Kavindi Madduma Hewage

      University of North Dakota

    Authors

    • Kavindi Madduma Hewage

      University of North Dakota

    • Carlos Miguel Munoz

      University of North Dakota

    • Mehmet Ozdogan

      University of North Dakota

    • Nuri Oncel

      University of North Dakota

    • Catherine Brissette

      University of North akota

    • Yvonne Tourand

      University of North dakota

    • Timothy Casselli

      University of North dakota

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  • Single-molecule Protein Analysis Based on Engineered Nanopores

    ORAL

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    Publication: M. Zhang et al. Real-time detection of 20 amino acids and discrimination of pathologically relevant peptides with functionalized nanopore. 2024, Nature Methods, 21(4), 609–618.

    Presenters

    • Ming Zhang

      Sichuan University

    Authors

    • Ming Zhang

      Sichuan University

    • Chao Tang

      Sichuan University

    • Zichun Wang

      Sichuan University

    • Shanchuan Chen

      Sichuan University

    • Lu Chen

      Sichuan University

    • Jia Geng

      Sichuan University

    View abstract →