Abstract
In the battle against the ever-changing SARS-CoV-2 landscape, understanding the interactions between viral proteins and the human immune system is paramount as it helps to explain potential factors contributing to diverse immunological responses in infected individuals. In this study, we employed state-of-the-art molecular docking tools to conduct large-scale virtual screens, predicting the binding affinities between 64 human cytokines against 17 coronavirus nucleocapsid proteins. Our comprehensivein silicoanalyses reveal specific changes in cytokine-nucleocapsid protein interactions, shedding light on potential modulators of the host immune response during infection. These findings offer valuable insights into the molecular mechanisms underlying viral pathogenesis and may guide the future development of targeted interventions. This manuscript serves as insight into the comparison of deep learning based AlphaFold2-Multimer and the semi-physicochemical based HADDOCK for protein-protein docking. We show the two methods are complementary in their predictive capabilities. We also introduce a novel algorithm for rapidly assessing the binding interface of protein-protein docks using graph edit distance: graph-based residue assessment function (G-RAF). The high-performance computational framework presented here will not only aid in accelerating the discovery of effective interventions against emerging viral threats, but extend to other applications of high throughput protein-protein screens.
Publisher
Cold Spring Harbor Laboratory
Reference38 articles.
1. Brady Johnston , Yuxuan Zhuang , Yinying Yao , William McCorkindale , Johannes Elferich , Patrick Kunzmann Rich , Olivier Laprevote , Thibault Tubiana , Domenico Marson , James Hooker , Jessica A. Nash , and Joyce Kim . BradyAJohnston/MolecularNodes: v2.10.0 for Blender 3.5+, September 2023.
2. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway
3. Neutralising antibody activity against SARS-CoV-2 VOCs B.1.617.2 and B.1.351 by BNT162b2 vaccination
4. Emma B. Hodcroft . CoVariants: SARS-CoV-2 Mutations and Variants of Interest, 2021.
5. Rapid assessment of SARS-CoV-2–evolved variants using virus-like particles
Cited by
1 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献