ArticleJournal of chemical theory and computation2019
Predicting Protein Dimer Structures Using MELD × MD.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
8 citing papers in PubMed, 16 citations in OpenAlex.
- MELD in Action: Harnessing Data to Accelerate Molecular Dynamics.Journal of chemical information and modeling · 2025Review
- Assessing a computational pipeline to identify binding motifs to theFrontiers in chemistry · 2023Article
- Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.Journal of chemical theory and computation · 2022Article
- Searching for Low Probability Opening Events in a DNA Sliding Clamp.Life (Basel, Switzerland) · 2022Article
- Characterization of sclerostin's response within white adipose tissue to an obesogenic diet at rest and in response to acute exercise in male mice.Frontiers in physiology · 2022Article
- Identifying hydrophobic protein patches to inform protein interaction interfaces.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Computing Ligands Bound to Proteins Using MELD-Accelerated MD.Journal of chemical theory and computation · 2020Article
- Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45.Proteins · 2020Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
It is challenging to predict the docked conformations of two proteins. Current methods are susceptible to errors from treating proteins as rigid bodies and from an inability to compute relative Boltzmann populations of different docked conformations. Here, we show that by using the ClusPro server as a front end to generate possible protein-protein contacts, and using Modeling Employing Limited Data (MELD) accelerated molecular dynamics (MELD × MD) as a back end for atomistic simulations, we can find 16/20 native dimer structures of small proteins as those having the lowest free energy, starting from good-bound-backbone structures. We show that atomistic MD free energies can be used to identify native protein dimer structures.
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Registered trials
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