ArticleBiomedical engineering online2016
Computer prediction of paratope on antithrombotic antibody 10B12 and epitope on platelet glycoprotein VI via molecular dynamics simulation.
Article in Biomedical engineering online, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed, 17 citations in OpenAlex.
- Mapping the epitope of PD-L1 to the paratope of the antibody durvalumab using molecular dynamics simulation.American journal of translational research · 2024Article
- Targeting Ras-binding domain of ELMO1 by computational nanobody design.Communications biology · 2023Article
- Comparison of Intermolecular Interactions of Irreversible and Reversible Inhibitors with Bruton's Tyrosine Kinase via Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2022Article
- Investigating the Role of the N-Terminal Loop of PD-1 in Binding Process Between PD-1 and Nivolumab via Molecular Dynamics Simulation.Frontiers in molecular biosciences · 2020Article
- Insight into Structural Characteristics of Protein-Substrate Interaction in Pimaricin Thioesterase.International journal of molecular sciences · 2019Article
- Preface: Computational and experimental methods for biological research: cardiovascular diseases and beyond.Biomedical engineering online · 2016Article
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Authors and funding
6 authors at 1 institution in 1 country.
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Abstract
backgroundInteraction between immunoglobulin-like receptor glycoprotein VI (GPVI) and collagen plays a central role in platelet activation and sequent firm adhesion. Of various antithrombotic agents targeting GPVI, antibody 10B12 is of great potential to block the GPVI-collagen interaction, but less is known about 10B12 paratope and GPVI epitope.
methodsAlong the pathway in the computer strategy presented in our previous work, the 10B12/GPVI complex model was constructed through homology modeling and rigid-body docking, and the molecular dynamics (MD) simulation was used to detect the paratope residues on 10B12 and their partners on GPVI. Quantified by free and steered MD simulations, the stabilities of hydrogen bonds and salt bridges were used to rank the contributions of interface residues to binding of 10B12 and GPVI.
resultsWe predicted 12 key and seven dispensable residues in interaction of 10B12 to GPVI with present computational procedure. Besides of the 12 key residues, two are epitope residues (LYS
conclusionsThe present computer strategy combining homology modeling, rigid body docking and MD simulation was illustrated to be effective in mapping paratope on antithrombotic antibody 10B12 to epitope on GPVI, and have large potential in drug discovery and antibody research.
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