ArticlePloS one2017
Elastic network model of learned maintained contacts to predict protein motion.
Article in PloS one, 2017. 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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Who cites it
6 citing papers in PubMed.
- Article
- Explicit versus implicit consideration of binding partners in protein-protein complex to elucidate intrinsic dynamics.Biophysical reviews · 2022Review
- PSP-GNM: Predicting Protein Stability Changes upon Point Mutations with a Gaussian Network Model.International journal of molecular sciences · 2022Article
- Review
- Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.International journal of molecular sciences · 2018Review
- Advances in coarse-grained modeling of macromolecular complexes.Current opinion in structural biology · 2018Review
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a novel elastic network model, lmcENM, to determine protein motion even for localized functional motions that involve substantial changes in the protein's contact topology. Existing elastic network models assume that the contact topology remains unchanged throughout the motion and are thus most appropriate to simulate highly collective function-related movements. lmcENM uses machine learning to differentiate breaking from maintained contacts. We show that lmcENM accurately captures functional transitions unexplained by the classical ENM and three reference ENM variants, while preserving the simplicity of classical ENM. We demonstrate the effectiveness of our approach on a large set of proteins covering different motion types. Our results suggest that accurately predicting a "deformation-invariant" contact topology offers a promising route to increase the general applicability of ENMs. We also find that to correctly predict this contact topology a combination of several features seems to be relevant which may vary slightly depending on the protein. Additionally, we present case studies of two biologically interesting systems, Ferric Citrate membrane transporter FecA and Arachidonate 15-Lipoxygenase.
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Registered trials
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