Physics of Proteins: Design & Prediction

Presentations

• Global epistasis from a physical learning perspective

  ORAL

  March 19, 2025, 2:30 PM – March 19, 2025, 2:42 PM

  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 →

• Machine Learning-Enhanced Predictions of Transcription Factor-DNA Binding Stability in Genomic Contexts

  ORAL

  March 19, 2025, 2:42 PM – March 19, 2025, 2:54 PM

  Publication: Machine Learning-Enhanced Predictions of Transcription Factor-DNA Binding Stability in Genomic Contexts (planned paper)

  Presenters

  • Carmen Al Masri

    University of California, Irvine

  Authors

  • Carmen Al Masri

    University of California, Irvine

  • Jin Yu

    University of California, Irvine

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• Designing a Protein-Protein Interface Scoring Function Using Graph Neural Networks

  ORAL

  March 19, 2025, 2:54 PM – March 19, 2025, 3:06 PM

  Presenters

  • Naomi Brandt

    Yale University

  Authors

  • Naomi Brandt

    Yale University

  • Jacob Sumner

    Yale University

  • Devon Finlay

    Yale University

  • Corey S O'Hern

    Yale University

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

  ORAL · Invited

  March 19, 2025, 3:06 PM – March 19, 2025, 3:42 PM

  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<br><br>[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<br><br>[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<br><br>[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

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

  ORAL

  March 19, 2025, 3:42 PM – March 19, 2025, 3:54 PM

  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<br>2. Wijerathne T., Bhatt A., Jiang W., Luo Y., Lacroix J., Mammalian PIEZO channels rectify anionic currents, bioRxiv, 2024.08. 23.609388, 2024<br>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<br>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 <br>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<br>6. Jiang, W., Ling, Y., Luo, Y., Mechanical properties of anionic asymmetric bilayers from atomistic simulations, J. Chem. Phys., 2021<br>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 →

• The relevance of vibrational modes in flexible docking of proteins

  ORAL

  March 19, 2025, 3:54 PM – March 19, 2025, 4:06 PM

  Presenters

  • Devon Finlay

    Yale University

  Authors

  • Devon Finlay

    Yale University

  • Jacob Sumner

    Yale University

  • Corey S O'Hern

    Yale University

  View abstract →

• Measuring the Interaction Radius of Proteins Using Small-Angle Scattering

  ORAL

  March 19, 2025, 4:06 PM – March 19, 2025, 4:18 PM

  Presenters

  • Chelsea E Edwards

    National Institute of Standards and Technology (NIST)

  Authors

  • Chelsea E Edwards

    National Institute of Standards and Technology (NIST)

  • Guangcui Yuan

    National Institute of Standards and Technology (NIST)

  • Yun Liu

    National Institute of Standards and Technology (NIST)

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• Target Prediction and Ligand Selectivity Using Inverse Virtual Screening for Structure-Based Drug Design

  ORAL

  March 19, 2025, 4:18 PM – March 19, 2025, 4:30 PM

  Presenters

  • Abeeb Ajibade

    University of Missouri - Columbia

  Authors

  • Abeeb Ajibade

    University of Missouri - Columbia

  • Xianjin Xu

    University of Missouri - Columbia

  • Xiaoqin Zou

    University of Missouri

  View abstract →

• Queuing theory models of competitive protein-protein interactions

  ORAL

  March 19, 2025, 4:30 PM – March 19, 2025, 4:42 PM

  Presenters

  • Yuming Jiang

    Syracuse University

  Authors

  • Yuming Jiang

    Syracuse University

  • Antun Skanata

    Syracuse University

  • Liviu Movileanu

    Syracuse University

  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

  March 19, 2025, 4:42 PM – March 19, 2025, 4:54 PM

  Publication: 1. AGUILAR PINEDA GE and OLIVARES QUIROZ L. Phys Biol, 18, 066002, (2021). DOI: 10.1088/1478-3975/ac211b. <br>2. OLIVARES QUIROZ L. Journal of Complex Networks, Volume 12, Issue 4, August 2024, cnae033, https://doi.org/10.1093/comnet/cnae033<br>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 →

• Biophysical Principles Predict Fitness of SARS-CoV-2 Variants

  ORAL

  March 19, 2025, 4:54 PM – March 19, 2025, 5:06 PM

  Publication: https://www.pnas.org/doi/abs/10.1073/pnas.2314518121

  Presenters

  • Dianzhuo Wang

    Harvard University

  Authors

  • Dianzhuo Wang

    Harvard University

  • Marian Huot

    Harvard University

  • Vaibhav Mohanty

    Harvard University/MIT

  • Eugene I Shakhnovich

    Harvard University

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

  ORAL

  March 19, 2025, 5:06 PM – March 19, 2025, 5:18 PM

  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

  View abstract →

• Single-molecule Protein Analysis Based on Engineered Nanopores

  ORAL

  March 19, 2025, 5:18 PM – March 19, 2025, 5:30 PM

  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 →