Academic Journal
Atomic-level evolutionary information improves protein-protein interface scoring
| العنوان: | Atomic-level evolutionary information improves protein-protein interface scoring |
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| المؤلفون: | Quignot, Chloé, Granger, Pierre, Chacón, Pablo, Guerois, Raphael, Andreani, Jessica |
| المساهمون: | Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences du Vivant Frédéric JOLIOT (JOLIOT), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Cientificas España = Spanish National Research Council Spain (CSIC), ANR-15-CE11-0008,CHIPSeT,Caracterisation Structurale des Couplages entre Chromatine et Homeostasie Protéique par Combinaison d'Analyses de Coevolution et de Perturbation des Interfaces de Complexes a Haut-Debit(2015), ANR-18-CE45-0005,ESPRINet,Intégration de données hétérogènes évolutives, structurales et omiques pour la prédiction des réseaux d'interaction protéine-ARN(2018) |
| المصدر: | ISSN: 1367-4803. |
| بيانات النشر: | CCSD Oxford University Press (OUP) |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | protein-protein interactions, protein docking, protein scoring, protein evolution, protein structure, structural bioinformatics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics |
| الوصف: | International audience ; Motivation: The crucial role of protein interactions and the difficulty in characterising them experimentally strongly motivates the development of computational approaches for structural prediction. Even when protein-protein docking samples correct models, current scoring functions struggle to discriminate them from incorrect decoys. The previous incorporation of conservation and coevolution information has shown promise for improving protein-protein scoring. Here, we present a novel strategy to integrate atomic-level evolutionary information into different types of scoring functions to improve their docking discrimination.Results: We applied this general strategy to our residue-level statistical potential from InterEvScore and to two atomic-level scores, SOAP-PP and Rosetta interface score (ISC). Including evolutionary information from as few as ten homologous sequences improves the top 10 success rates of individual atomic-level scores SOAP-PP and Rosetta ISC by respectively 6 and 13.5 percentage points, on a large benchmark of 752 docking cases. The best individual homology-enriched score reaches a top 10 success rate of 34.4%. A consensus approach based on the complementarity between different homology-enriched scores further increases the top 10 success rate to 40%.Availability: All data used for benchmarking and scoring results, as well as a Singularity container of the pipeline, are available at http://biodev.cea.fr/interevol/interevdata/Contact: jessica.andreani@cea.fr or guerois@cea.frSupplementary information: Supplementary data are available at Bioinformatics online. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| Relation: | BIORXIV: 2020.10.26.355073 |
| DOI: | 10.1093/bioinformatics/btab254 |
| الاتاحة: | https://cea.hal.science/cea-02978447 https://cea.hal.science/cea-02978447v2/document https://cea.hal.science/cea-02978447v2/file/202104_Quignot_et_al_AM.pdf https://doi.org/10.1093/bioinformatics/btab254 |
| Rights: | info:eu-repo/semantics/OpenAccess |
| رقم الانضمام: | edsbas.6A32B33C |
| قاعدة البيانات: | BASE |
| DOI: | 10.1093/bioinformatics/btab254 |
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