Machine Learning Tools Advance Biophysics

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 2024 Aug 22

PMID 39173628

Authors

Tamar Schlick

Guo-Wei Wei

Affiliations

Soon will be listed here.

References

Schlick T, Portillo-Ledesma S . Biomolecular modeling thrives in the age of technology. Nat Comput Sci. 2021; 1(5):321-331. PMC: 8378674. DOI: 10.1038/s43588-021-00060-9. View

Barcenas M, Bocci F, Nie Q . Tipping points in epithelial-mesenchymal lineages from single-cell transcriptomics data. Biophys J. 2024; 123(17):2849-2859. PMC: 11393678. DOI: 10.1016/j.bpj.2024.03.021. View

Gorin G, Carilli M, Chari T, Pachter L . Spectral neural approximations for models of transcriptional dynamics. Biophys J. 2024; 123(17):2892-2901. PMC: 11393700. DOI: 10.1016/j.bpj.2024.04.034. View

Karolak A, Urbaniak K, Monastyrskyi A, Duckett D, Branciamore S, Stewart P . Structure-independent machine-learning predictions of the CDK12 interactome. Biophys J. 2024; 123(17):2910-2920. PMC: 11393676. DOI: 10.1016/j.bpj.2024.05.017. View

Verma A, Ray K, Bodick M, Kinz-Thompson C, Gonzalez Jr R . Increasing the accuracy of single-molecule data analysis using tMAVEN. Biophys J. 2024; 123(17):2765-2780. PMC: 11393709. DOI: 10.1016/j.bpj.2024.01.022. View

Risheh A, Rebel A, Nerenberg P, Forouzesh N . Calculation of protein-ligand binding entropies using a rule-based molecular fingerprint. Biophys J. 2024; 123(17):2839-2848. PMC: 11393669. DOI: 10.1016/j.bpj.2024.03.017. View

Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G . MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction. Biophys J. 2024; 123(17):2902-2909. PMC: 11393670. DOI: 10.1016/j.bpj.2024.05.011. View

Guo W, Du D, Zhang H, Sanchez J, Sun S, Xu W . Bound ion effects: Using machine learning method to study the kinesin Ncd's binding with microtubule. Biophys J. 2023; 123(17):2740-2748. PMC: 11393710. DOI: 10.1016/j.bpj.2023.12.024. View

Mitchell E, Story B, Boothe D, Franaszczuk P, Maroulas V . A topological deep learning framework for neural spike decoding. Biophys J. 2024; 123(17):2781-2789. PMC: 11393671. DOI: 10.1016/j.bpj.2024.01.025. View

10.

Liu J, Xu S, He P, Wu S, Luo X, Deng Y . VSG-GAN: A high-fidelity image synthesis method with semantic manipulation in retinal fundus image. Biophys J. 2024; 123(17):2815-2829. PMC: 11393672. DOI: 10.1016/j.bpj.2024.02.019. View

11.

Dasetty S, Bidone T, Ferguson A . Data-driven prediction of αβ integrin activation paths using manifold learning and deep generative modeling. Biophys J. 2023; 123(17):2716-2729. PMC: 11393677. DOI: 10.1016/j.bpj.2023.12.009. View

12.

Zhang Y, Yang C, Xiong Y, Xiao Y . 3dDNAscoreA: A scoring function for evaluation of DNA 3D structures. Biophys J. 2024; 123(17):2696-2704. PMC: 11393702. DOI: 10.1016/j.bpj.2024.02.018. View

13.

Sharma K, Doktorova M, Waxham M, Heberle F . Cryo-EM images of phase-separated lipid bilayer vesicles analyzed with a machine-learning approach. Biophys J. 2024; 123(17):2877-2891. PMC: 11393711. DOI: 10.1016/j.bpj.2024.04.029. View

14.

Smith K, Oglietti R, Moran S, Macosko J, Lyles D, Holzwarth G . Directional change during active diffusion of viral ribonucleoprotein particles through cytoplasm. Biophys J. 2024; 123(17):2869-2876. PMC: 11393665. DOI: 10.1016/j.bpj.2024.04.025. View

15.

Chen J, Xu Y, Yang X, Cang Z, Geng W, Wei G . Poisson-Boltzmann-based machine learning model for electrostatic analysis. Biophys J. 2024; 123(17):2807-2814. PMC: 11393697. DOI: 10.1016/j.bpj.2024.02.008. View

16.

Abarca-Ortega A, Gonzalez-Bermudez B, Plaza G . Enhancing micropipette aspiration with artificial-intelligence analysis. Biophys J. 2024; 123(17):2860-2868. PMC: 11393679. DOI: 10.1016/j.bpj.2024.04.006. View

17.

Zhang S, Li J, Chen S . Machine learning in RNA structure prediction: Advances and challenges. Biophys J. 2024; 123(17):2647-2657. PMC: 11393687. DOI: 10.1016/j.bpj.2024.01.026. View

18.

Satalkar V, Degaga G, Li W, Pang Y, McShan A, Gumbart J . Generative β-hairpin design using a residue-based physicochemical property landscape. Biophys J. 2024; 123(17):2790-2806. PMC: 11393682. DOI: 10.1016/j.bpj.2024.01.029. View

19.

Rollins Z, Widatalla T, Cheng A, Metwally E . AbMelt: Learning antibody thermostability from molecular dynamics. Biophys J. 2024; 123(17):2921-2933. PMC: 11393704. DOI: 10.1016/j.bpj.2024.06.003. View

20.

King J, Koes D . Interpreting forces as deep learning gradients improves quality of predicted protein structures. Biophys J. 2023; 123(17):2730-2739. PMC: 11393680. DOI: 10.1016/j.bpj.2023.12.011. View