CARBONE, A. | bioRxiv Science

bioRxiv2021

DLA-Ranker: Evaluating protein docking conformations with many locally oriented cubes.

Proteins ensure their biological functions by interacting with each other, and with other molecules. Determining the relative position and orientation of protein partners in a complex remains challenging. Here, we address the problem of ranking candidate complex conformations toward identifying near-native conformations. We propose a deep learning approach relying on a local representation of the protein interface with an explicit account of its geometry. We show that the method is able to recognise certain pattern distributions in specific locations of the interface. We compare and combine it with a physics-based scoring function and a statistical pair potential.

bioinformatics↗

bioRxiv2021

LEVELNET: diving into the multiple layers of protein-protein physical interaction networks

AO_SCPLOWBSTRACTC_SCPLOWPhysical interactions between proteins are central to all biological processes. Yet, the current knowledge of who interacts with whom in the cell and in what manner relies on partial, noisy, and highly heterogeneous data. Thus, there is a need for methods comprehensively describing and organising such data. LEVELNET is a versatile and interactive tool for visualising, exploring and comparing protein-protein interaction (PPI) networks inferred from different types of evidence. LEVELNET helps to break down the complexity of PPI networks by representing them as multilayered graphs and by facilitating the direct comparison of their subnetworks toward biological interpretation. It focuses primarily on the protein chains whose 3D structures are available in the Protein Data Bank. We showcase some potential applications, such as investigating the structural evidence supporting PPIs associated to specific biological processes, assessing the co-localisation of interaction partners, comparing the PPI networks obtained through computational experiments versus homology transfer, and creating PPI benchmarks with desired properties. Availability: LEVELNET is freely available to the community at http://www.lcqb.upmc.fr/levelnet/.

bioinformatics↗