ArticleStructure (London, England : 1993)2008
Ab initio folding of proteins with all-atom discrete molecular dynamics.
Article in Structure (London, England : 1993), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 203 papers.
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Who cites it
203 citing papers in PubMed.
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- Parallel in-register contact propensity predicts the Amyloidogenicity of ADan and ABri in familial dementias.International journal of biological macromolecules · 2026Article
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- The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives.Journal of molecular biology · 2025Review
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- The Glycine-Rich Region as a Flexible Molecular Glue Promoting hPrPJournal of chemical information and modeling · 2025Article
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- Microglial Clearance of Alzheimer's Amyloid-Beta Obstructed by Nanoplastics.Environmental science. Nano · 2025Article
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- Determinants for Substoichiometric Inhibition of IAPP and Aβ Amyloid Aggregations by Bri2 BRICHOS.ACS chemical neuroscience · 2025Article
- Computational insights into the aggregation mechanism of human calcitonin.International journal of biological macromolecules · 2025Article
- Impact of frequent ARID1A mutations on protein stability provides insights into cancer pathogenesis.Scientific reports · 2025Article
- Impact of Frequent ARID1A Mutations on Protein Stability: Insights into Cancer Pathogenesis.Research square · 2024Article
- Computational insights into the aggregation mechanism and amyloidogenic core of aortic amyloid medin polypeptide.Colloids and surfaces. B, Biointerfaces · 2024Article
- Exploring the Impact of Physiological C-Terminal Truncation on α-Synuclein Conformations to Unveil Mechanisms Regulating Pathological Aggregation.Journal of chemical information and modeling · 2024Article
- Islet amyloid polypeptide fibril catalyzes amyloid-β aggregation by promoting fibril nucleation rather than direct axial growth.International journal of biological macromolecules · 2024Article
143 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field featuring packing, solvation, and environment-dependent hydrogen bond interactions. We performed folding simulations of six small proteins (20-60 residues) with distinct native structures by the replica exchange method. In all cases, native or near-native states were reached in simulations. For three small proteins, multiple folding transitions are observed, and the computationally characterized thermodynamics are in qualitative agreement with experiments. The predictive power of all-atom DMD highlights the importance of environment-dependent hydrogen bond interactions in modeling protein folding. The developed approach can be used for accurate and rapid sampling of conformational spaces of proteins and protein-protein complexes and applied to protein engineering and design of protein-protein interactions.
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