ArticleLiving journal of computational molecular science2025
Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].
Article in Living journal of computational molecular science, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Progress toward linking single-molecule behavior and condensate material properties.Current opinion in structural biology · 2026Review
- Training a force field for proteins and small molecules from scratch.Chemical science · 2026Article
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Article
- Comparative Structural Analysis of Escherichia Coli Cyay at Room and Cryogenic Temperatures Using Macromolecular and Serial Crystallography.Chembiochem : a European journal of chemical biology · 2025Article
- Determining accurate conformational ensembles of intrinsically disordered proteins at atomic resolution.Nature communications · 2025Article
- Coil-Library-Derived Amino-Acid-Specific Side-Chain χJournal of chemical theory and computation · 2025Article
- Accuracy and Reproducibility of Lipari-Szabo Order Parameters From Molecular Dynamics.The journal of physical chemistry. B · 2024Article
- The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling.The journal of physical chemistry. B · 2024Article
- Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP.Communications biology · 2024Article
- Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase.bioRxiv : the preprint server for biology · 2023Article
- Weighted Ensemble Simulation: Advances in methods, software, and applications.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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Authors and funding
14 authors.
Funding
Abstract
This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature (RT) protein crystallography. We discuss what the observables are, what they tell us about structure and dynamics, what makes them useful for assessing force field accuracy, and how they can be connected to molecular dynamics simulations carried out using the force field one wishes to benchmark. We also touch on best practices for setup and analysis of benchmark simulations. We hope this article will be particularly useful to computational researchers and trainees who develop, benchmark, or use protein force fields or machine learning models that generate protein ensembles.
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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.