ArticleJournal of chemical theory and computation2012
Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
7 citing papers in PubMed, 26 citations in OpenAlex.
- Mechanistic Insights into Enzyme Catalysis from Explaining Machine-Learned Quantum Mechanical and Molecular Mechanical Minimum Energy Pathways.ACS physical chemistry Au · 2022Article
- QM/MM modeling of class A β-lactamases reveals distinct acylation pathways for ampicillin and cefalexin.Organic & biomolecular chemistry · 2021Article
- Unraveling the energetic significance of chemical events in enzyme catalysis via machine-learning based regression approach.Communications chemistry · 2020Article
- Hierarchical Markov State Model Building to Describe Molecular Processes.Journal of chemical theory and computation · 2020Article
- Large-Scale Conformational Changes and Protein Function: Breaking theFrontiers in molecular biosciences · 2019Review
- Role of magnesium ions in the reaction mechanism at the interface between Tm1631 protein and its DNA ligand.Chemistry Central journal · 2016Article
- QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes.Methods in enzymology · 2016Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Chain-of-state methods are becoming important tools in studying the chemical reaction mechanisms, especially for biomacromolecules. In this article, three chain-of-state methods, nudged elastic band (NEB) method and the replica path method with restraints or constraints, were tested and compared using three model systems with various sizes and at different levels of theory: alanine dipeptide isomerization, β-alanine intramolecular condensation, and the matrix metalloproteinase 2 inhibition mechanism. The levels of theory used to describe the three model systems include molecular mechanics (MM), quantum mechanics (QM), and combined quantum mechanics and molecular mechanics (QM/MM). All three methods could correctly determine a reaction path with reasonable estimation of reaction barriers in most cases. The RMSD measurement with additional weighting schemes provides practically infinite choices of reaction coordinates to describe the reaction progress. These findings demonstrate that the chain-of-state methods are powerful tools when being used carefully to generate a plausible reaction mechanism with full pathway for complex systems at an affordable computational cost.
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Registered trials
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