Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 13, Issue 3, Pages 1454-1461Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.6b01153
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Funding
- Spanish Ministry of Science [BFU2014-52864-R]
- Catalan SGR
- Instituto Nacional de Bioinformatica
- European Union's Horizon BioExcel and Elixir-Excellerate projects
- Biomolecular and Bioinformatics Resources Platform [ISCIII PT 13/0001/0030]
- Fondo Europeo de Desarrollo Regional (FEDER)
- MINECO Severo Ochoa Award of Excellence (Government of Spain)
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We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.
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