ArticleJournal of computational chemistry2016
Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling.
Article in Journal of computational chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Unveiling the KRAS Relationship between Affinity and Dynamics: A Molecular Simulations Study.Journal of chemical information and modeling · 2026Article
- An Automated Workflow for Diagnosing Sampling Issues Caused by Slow Torsional Motions in Molecular Simulations.Journal of chemical information and modeling · 2026Article
- Accelerated Enveloping Distribution Sampling (AEDS) Allows for Efficient Sampling of Orthogonal Degrees of Freedom.Journal of chemical information and modeling · 2023Article
- Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure.Journal of computer-aided molecular design · 2022Article
- Repulsive Soft-Core Potentials for Efficient Alchemical Free Energy Calculations.Journal of chemical theory and computation · 2020Article
- Comparison of free-energy methods using a tripeptide-water model system.Journal of computational chemistry · 2018Article
- Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling.Journal of computational chemistry · 2016Article
Corrections and comments
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3 authors.
Funding
Abstract
Previous free-energy calculations have shown that the seemingly simple transformation of the tripeptide KXK to KGK in water holds some unobvious challenges concerning the convergence of the forward and backward thermodynamic integration processes (i.e., hysteresis). In the current study, the central residue X was either alanine, serine, glutamic acid, lysine, phenylalanine, or tyrosine. Interestingly, the transformation from alanine to glycine yielded the highest hysteresis in relation to the extent of the chemical change of the side chain. The reason for that could be attributed to poor sampling of φ2 /ψ2 dihedral angles along the transformation. Altering the nature of alanine's Cβ atom drastically improved the sampling and at the same time led to the identification of high energy barriers as cause for it. Consequently, simple strategies to overcome these barriers are to increase simulation time (computationally expensive) or to use enhanced sampling techniques such as Hamiltonian replica exchange molecular dynamics and one-step perturbation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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