The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.
Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics
Open accessAbstract
Summary 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. Using the replica exchange method, we perform folding simulations of six small proteins (20–60 residues) with distinct native structures. In all cases, native or near-native states are reached in simulations. For three small proteins, multiple folding transitions are observed and the computationally-characterized thermodynamics are in quantitative 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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Metadata
- Authors
- Ding, F., Tsao, D., Nie, H., & Dokholyan, N. V.
- Venue
- Structure
- Publisher
- Elsevier BV
- Published
- 2008-07
- Volume
- 16
- Issue
- 7
- Pages
- 1010-1018
- ISSN
- 0969-2126 (ISSN-L)
- OpenAlex
- W2107696550
- Cited by
- 326
- References
- 45
- FWCI
- 5.09
- Type
- journal article
- Language
- en
- Open access
- bronze
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