ArticleLiving journal of computational molecular science2018
Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0].
Article in Living journal of computational molecular science, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 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
89 citing papers in PubMed.
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- Dynamic stability-driven machine learning improves binding pose identification on human serum albumin.Journal of computer-aided molecular design · 2026Article
- Uncertainty Quantification forChemical reviews · 2026Review
- Metal-Coordination Specificity and Structural Dynamics of C. elegans Metallothionein I: Insights From 3D Modeling and MD Simulations.Proteins · 2026Article
- Conformational dynamics of fuzzy interfaces in disordered protein complexes: mapping key residues and binding modes beyond NMR models.Frontiers in bioinformatics · 2026Article
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- Gaussian Accelerated Molecular Dynamics Simulations Combined with NRIMD to Explore the Mechanism of Substrate Selectivity of Cid1 Polymerase for Different Nucleoside Triphosphates.International journal of molecular sciences · 2025Article
- Integrated experimental and computational study reveals enhanced antimicrobial efficacy of amoxicillin loaded in oleic acid nanoemulsion against multidrug-resistantRSC advances · 2025Article
- A nonclassical pathway of β-hematin crystal nucleation enables its suppression by antimalarials.Communications chemistry · 2025Article
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- Robustness in biomolecular simulations: Addressing challenges in data generation, analysis, and curation.Cell reports. Physical science · 2025Article
- Lessons Learned on Obtaining Reliable Dynamic Properties for Ionic Liquids.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
- Pathogenic mutation impairs functional dynamics of Hsp60 in mono- and oligomeric states.Nature communications · 2025Article
- Prospective Evaluation of Structure-Based Simulations Reveal Their Ability to Predict the Impact of Kinase Mutations on Inhibitor Binding.The journal of physical chemistry. B · 2025Article
- Multiscale Interfacial Structure and Organization of sII Gas Hydrate Interfaces Using Molecular Dynamics.Nanomaterials (Basel, Switzerland) · 2025Article
29 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The quantitative assessment of uncertainty and sampling quality is essential in molecular simulation. Many systems of interest are highly complex, often at the edge of current computational capabilities. Modelers must therefore analyze and communicate statistical uncertainties so that "consumers" of simulated data understand its significance and limitations. This article covers key analyses appropriate for trajectory data generated by conventional simulation methods such as molecular dynamics and (single Markov chain) Monte Carlo. It also provides guidance for analyzing some 'enhanced' sampling approaches. We do not discuss
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.