ArticleJournal of chemical theory and computation2009
Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties.
Article in Journal of chemical theory and computation, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
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- Entropy Rules: Molecular Dynamics Simulations of Model Oligomers for Thermoresponsive Polymers.Entropy (Basel, Switzerland) · 2020Article
- Insights into the Effect of Curcumin and (-)-Epigallocatechin-3-Gallate on the Aggregation of Aβ(1-40) Monomers by Means of Molecular Dynamics.International journal of molecular sciences · 2020Article
- Significance of triple torsional correlations in proteins.RSC advances · 2019Article
- Structural mechanism of DNA-mediated Nanog-Sox2 cooperative interaction.RSC advances · 2019Article
- Computational Insight into the Effect of Natural Compounds on the Destabilization of Preformed Amyloid-β(1⁻40) Fibrils.Molecules (Basel, Switzerland) · 2018Article
- Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field.Physical chemistry chemical physics : PCCP · 2016Article
- Lupin Peptides Modulate the Protein-Protein Interaction of PCSK9 with the Low Density Lipoprotein Receptor in HepG2 Cells.Scientific reports · 2016Article
- Conformational Entropy of Intrinsically Disordered Proteins from Amino Acid Triads.Scientific reports · 2015Article
- On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.Proteins · 2015Article
- Current and emerging opportunities for molecular simulations in structure-based drug design.Physical chemistry chemical physics : PCCP · 2014Article
- Conformational contribution to thermodynamics of binding in protein-peptide complexes through microscopic simulation.Biophysical journal · 2013Article
- Retention of conformational entropy upon calmodulin binding to target peptides is driven by transient salt bridges.Biophysical journal · 2012Article
- Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion.Journal of chemical theory and computation · 2012Article
- Accurate prediction of the binding free energy and analysis of the mechanism of the interaction of replication protein A (RPA) with ssDNA.Journal of molecular modeling · 2012Article
- Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition.Quarterly reviews of biophysics · 2012Review
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Authors and funding
3 authors.
Funding
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Abstract
The convergence properties of the absolute single-molecule configurational entropy and the correction terms used to estimate it are investigated using microsecond molecular dynamics simulation of a peptide test system and an improved methodology. The results are compared with previous applications for systems of diverse chemical nature. It is shown that (i) the effect of anharmonicity is small, (ii) the effect of pairwise correlation is typically large, and (iii) the latter affects to a larger extent the entropy estimate of thermodynamic states characterized by a higher motional correlation. The causes of such deviations from a quasi-harmonic behavior are explained. This improved approach provides entropies also for molecular systems undergoing conformational transitions and characterized by highly frustrated energy surfaces, thus not limited to systems sampling a single quasi-harmonic basin. Overall, this study emphasizes the need for extensive phase-space sampling in order to obtain a reliable estimation of entropic contributions.
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