Journal club

Journal club meetings are on Mondays at 2-3 pm through video conference.

May 19, 2021
Arginine multivalency stabilizes protein/RNA condensates

M. Paloni, G. Bussi, and A. Barducci (2021) bioRxiv doi: https://doi.org/10.1101/2021.04.22.440959

Abstract PDF

presented by Gilberto

May 12, 2021
Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics

Wang D, Zhang L, Wang H, E W. arXiv. 2021.

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presented by Lim

May 5, 2021
Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins

Greener and Jones, (2021) bioRxiv

Abstract | PDF

Presented by Giacomo

April 28, 2021
Sequence-encoded and composition-dependent protein-RNA interactions control multiphasic condensate morphologies

Kaur, T., Raju, M., Alshareedah, I. et al. Nat Commun 12, 872 (2021). https://doi.org/10.1038/s41467-021-21089-4

Abstract PDF | SI

presented by Gilberto

April 21, 2021
Predicting new protein conformations from molecular dynamics simulation conformational landscapes and machine learning

Yiming Jin, Linux O. Johannissen, Sam Hay: Prediction new protein conformations from molecular dynamics simulation conformational landscapes and machine learning. Proteins (2021)

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presented by Michael

April 21, 2021
MSA Transformer

Rao R, Liu J, Verkuil R, Meier J, Canny JF, Abbeel P, et al. MSA Transformer. bioRxiv. 2021.

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presented by Lim

April 14, 2021
Protein sequence design by conformational landscape optimization

Norn et al., (2021) PNAS

Abstract | PDF | SI

Presented by Giacomo

April 7, 2021
FtsZ-Induced shape transformation of coacervates

Fanalista, F., Deshpande, S., Lau, A., Pawlik, G., & Dekker, C. (2018). Advanced Biosystems2(9), 1800136. https://doi.org/10.1002/adbi.201800136

Abstract PDF | SI

presented by Gilberto

March 24, 2021
Mechanistic basis for ubiquitin modulation of a protein energy landscape

Carroll, E.C., Latorraca, N.R., Lindner, J.M., Maguire, B.C., Pelton, J.G., and Marqusee, S. Proc. Natl. Acad. Sci. U.S.A. (2021).

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presented by Lim

March 17, 2021
Discovery of a hidden transient state in all bromodomain families

Raich et al., (2021) PNAS

Abstract | PDF | SI

Presented by Giacomo

March 3, 2021
Spontaneous driving forces give rise to protein‚ąíRNA condensates with coexisting phases and complex material properties

Boeynaems, S., Holehouse, A. S., Weinhardt, V., et al. (2019). PNAS, 116(16), 7889–7898. https://doi.org/10.1073/pnas.1821038116

Abstract PDF | SI

presented by Gilberto

February 17, 2021
Extraction of protein dynamics information from cryo-EM maps using deep learning

Matsumoto et al., Nature Machine Intelligence (2021).

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presented by Lim

February 10, 2021
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

Gainza et al., (2020) Nature Methods

Abstract | PDF | SI

Presented by Giacomo

February 3, 2021
Lysine/RNA-interactions drive and regulate biomolecular condensation

Ukmar-Godec, T., Hutten, S., Grieshop, M.P. et al. Nat Commun 10, 2909 (2019) https://doi.org/10.1038/s41467-019-10792-y

Abstract PDF | SI

presented by Gilberto

January 27, 2021
Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds

Thomas et al., arXiv (2018).

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presented by Lim

January 20, 2021
Fast and effective protein model refinement by deep graph neural networks

Xiaoyang Jing and Jinbo Xu (2020) bioRxiv,

January 13, 2021
Competing Protein-RNA Interaction Networks Control Multiphase Intracellular Organization

Sanders, D. W., et al (2020) Cell181(2), 306-324.e28, doi.org/10.1016/j.cell.2020.03.050

Abstract PDF | SI

presented by Gilberto

January 6, 2021
Genetic interaction mapping informs integrative structure determination of protein complexes

Braberg et al., Science (2020).

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presented by Lim

December 16, 2020
Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations

Zheng, W., et al. (2020). JPC B, acs.jpcb.0c10489

Abstract PDF | SI

presented by Gilberto

December 9, 2020
Refining All-Atom Protein Force Fields for Polar-Rich, Prion-like, Low-Complexity Intrinsically Disordered Proteins

W. S. Tang, N. L. Fawzi, and J. Mittal
J. Phys. Chem. B 2020, 124, 9505−9512

Abstract / PDF

presented by Bercem