ArticleComputational and structural biotechnology journal2021
Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization.
Article in Computational and structural biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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- The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics.Journal of chemical theory and computation · 2024Article
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2 authors at 1 institution in 1 country.
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Abstract
Continuous assessment of transferable forcefields for molecular simulations is essential to identify their weaknesses and direct improvement efforts. The latest efforts focused on better describing disordered proteins while retaining proper description of folded domains, important because forcefields of the previous generations produce overly compact disordered states. Such improvements should additionally alleviate the related problem of over-stabilized protein-protein interactions, which has been largely overlooked. Here we evaluated three state-of-the-art forcefields, current flagships of their respective developers, optimized for ordered and disordered proteins: CHARMM36m with its recommended corrected TIP3P* water, ff19SB with the recommended OPC water, and the 2019 a99SBdisp forcefield by D. E. Shaw Research with its modified TIP4P water; plus ff14SB with TIP3P as an example of the former generation of forcefields. Our evaluation entailed simulations of (i) multiple copies of a protein that is highly soluble yet undergoes weak dimerization, (ii) a disordered peptide with low, well-characterized alpha helical propensity, and (iii) a peptide known to form insoluble β-aggregates. Our results recapitulate ff14SB-TIP3P over-stabilizing aggregates and secondary structures and place a99SBdisp-TIP4PD at the other end
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