ArticlePLoS computational biology2013
A tunable coarse-grained model for ligand-receptor interaction.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 29 citations in OpenAlex.
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- Modular analysis of the control of flagellar Ca2+-spike trains produced by CatSper and CaV channels in sea urchin sperm.PLoS computational biology · 2020Article
- Mechanisms of noncanonical binding dynamics in multivalent protein-protein interactions.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Drug treatment efficiency depends on the initial state of activation in nonlinear pathways.Scientific reports · 2018Article
- Computationally Efficient Modelling of Stochastic Spatio-Temporal Dynamics in Biomolecular Networks.Scientific reports · 2018Article
- General principles of binding between cell surface receptors and multi-specific ligands: A computational study.PLoS computational biology · 2017Article
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- Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants.Annals of botany · 2014Review
- Modelling effects of internalized antibody: a simple comparative study.Theoretical biology & medical modelling · 2014Article
- Tuneable resolution as a systems biology approach for multi-scale, multi-compartment computational models.Wiley interdisciplinary reviews. Systems biology and medicineReview
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell-surface receptors are the most common target for therapeutic drugs. The design and optimization of next generation synthetic drugs require a detailed understanding of the interaction with their corresponding receptors. Mathematical approximations to study ligand-receptor systems based on reaction kinetics strongly simplify the spatial constraints of the interaction, while full atomistic ligand-receptor models do not allow for a statistical many-particle analysis, due to their high computational requirements. Here we present a generic coarse-grained model for ligand-receptor systems that accounts for the essential spatial characteristics of the interaction, while allowing statistical analysis. The model captures the main features of ligand-receptor kinetics, such as diffusion dependence of affinity and dissociation rates. Our model is used to characterize chimeric compounds, designed to take advantage of the receptor over-expression phenotype of certain diseases to selectively target unhealthy cells. Molecular dynamics simulations of chimeric ligands are used to study how selectivity can be optimized based on receptor abundance, ligand-receptor affinity and length of the linker between both ligand subunits. Overall, this coarse-grained model is a useful approximation in the study of systems with complex ligand-receptor interactions or spatial constraints.
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