3DOR 2024 - Short Papers

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https://diglib.eg.org/handle/10.2312/3607033

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Browsing 3DOR 2024 - Short Papers by Subject "Applied computing → Molecular structural biology"

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    SHREC2024: Non-rigid Complementary Shapes Retrieval in Protein-protein Interactions
    (The Eurographics Association, 2024) Yacoub, Taher; Zarubina, Nika; Depenveiller, Camille; Nguyen, Hoang-Phuc; Vong, Vinh-Toan; Tran, Minh-Triet; Kagaya, Yuki; Nakamura, Tsukasa; Kihara, Daisuke; Langenfeld, Florent; Montes, Matthieu; Biasotti, Silvia; Bustos, Benjamin; Schreck, Tobias; Sipiran, Ivan; Veltkamp, Remco C.
    The aim of this SHREC 2024 track is to compare different algorithms for retrieving non-rigid complementary shape pairs, applied in the context of 3D objects being more complex (e.g. with many folds and roughness) such as proteins. The dataset used for this benchmark is based on 52 selected protein-protein complexes for which an experimental structure is publicly available. One of the main difficulties of this challenge is the non-inclusion of the shapes derived from the ground truth conformations in the dataset. Different metrics were used to evaluate the retrieval performance (nearest-neighbor, first-tier, second-tier, and true positives) and to evaluate the quality of the predicted poses (TM-score, lDDT, ICS, IPS and DockQ - those metrics are classically used in the Critical Assessment of PRediction of Interactions challenges). Two teams took part in this challenge and were able to return the expected results. This paper discusses these results and prospects of retrieval methods based only on the protein shape information in the absence of atomic data, in a large context of protein-protein docking.