Predicting Epitopes of Synthetic Binding Proteins Using Protein Structure Prediction and Protein-Protein Docking.

Arzu Mijit, Yanlin Li, Weiwei Xue

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

3 authors.

Arzu MijitChongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China.

Yanlin LiChongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China.

Weiwei XueChongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China. xueww@cqu.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Synthetic binding proteins (SBPs) engineered from privileged protein scaffolds usually have high specificity to protein target. However, epitope information of currently known SBPs is still limited, which hinders the development of protein binders with desired function. Herein, a framework combining protein structure prediction (AlphaFold2) and protein-protein docking (HawkDock and RosettaDock) was designed for predicting the epitope of specific SBP. Using the experimental structure of a nanobody in complex with SARS-CoV-2 receptor binding domain (RBD) as an example, the computational framework perfectly reproduced the binding mode between the SBP and target protein. Therefore, the strategy can be expanded to predict the epitopes of other SBPs, which may provide useful information for understanding the molecular mechanism of protein-protein recognition, but also facilitate the rational design of novel SBPs with enhanced properties.

Indexed as

EpitopesMolecular Docking SimulationSpike Glycoprotein, CoronavirusBinding SitesComputational BiologyCOVID-19HumansProtein BindingProtein ConformationSARS-CoV-2Single-Domain AntibodiesEpitopesSingle-Domain AntibodiesSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2EpitopeProtein designProtein-protein dockingProtein structure predictionSynthetic binding protein

Identifiers

PMID40593425

DOI10.3390/md20050307

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.