ArticleJournal of chemical theory and computation2018
MELD × MD Folds Nonthreadables, Giving Native Structures and Populations.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices.Journal of chemical theory and computation · 2024Article
- Structure Determination of Challenging Protein-Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations.Journal of chemical information and modeling · 2023Article
- Accelerating Protein Folding Molecular Dynamics Using Inter-Residue Distances from Machine Learning Servers.Journal of chemical theory and computation · 2022Article
- Structure-based protein design with deep learning.Current opinion in chemical biology · 2021Review
- MELD-accelerated molecular dynamics help determine amyloid fibril structures.Communications biology · 2021Article
- Binding Ensembles ofMolecules (Basel, Switzerland) · 2021Article
- Protein storytelling through physics.Science (New York, N.Y.) · 2020Review
- 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
- NMR-assisted protein structure prediction with MELDxMD.Proteins · 2019Article
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Authors and funding
3 authors.
Funding
Abstract
A current challenge is to compute the native structures of proteins from their amino acid sequences. A main approach of bioinformatics is threading, in which a protein to be predicted is computationally threaded onto protein fragments of similar sequence having an already known structure. However, ∼15% of proteins cannot be folded in this way; this has been called the glass ceiling, and the proteins are called nonthreadables. For these, physical molecular dynamics (MD) modeling is promising because it does not require templates. We find that MD, when used with an accelerator called MELD, can fold many nonthreadables. For 41 nonthreadable proteins with fewer than 125 residues, MELD-accelerated MD (MELD × MD) folds 20 of them to better than 4 Å error. In 10 cases, MELD × MD succeeds even when the force field does not properly encode the native state. In 11 cases, MELD × MD foretells its own success; seeing large Boltzmann populations in the simulations predicts it has converged to the correct native state. MELD × MD acceleration can be applied to a broad physical protein modeling range.
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