ArticleScientific reports2026
High resolution mapping of protein motions in time and space with RMSX and Flipbook.
Article in Scientific reports, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Deep learning-guided high-throughput screening and molecular dynamics simulations facilitate the discovery of potential FXIIa inhibitors.Journal of molecular modeling · 2026Article
- Mapping the TCR landscape: computational tools empowering translational immunology and therapy design.Journal for immunotherapy of cancer · 2026Review
- Synthesis, characterization, and α-glucosidase inhibitory activity of methyl proline derivatives of phenylpropanoid.RSC advances · 2026Article
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Authors and funding
3 authors.
Funding
Abstract
Demonstrating when and where proteins undergo conformational rearrangement remains challenging in molecular dynamics (MD) analysis, particularly for transient and localized motions. We introduce RMSX, a time-series extension of root-mean-square fluctuation (RMSF), and Flipbook, a general-purpose method for mapping simulation metrics onto structural, atomistic snapshots. Unlike traditional RMSF values, RMSX is performed over partitions of the original simulation - not its entirety. This simple extension allows RMSX to pinpoint not only the degree of fluctuation but also isolate when a significant motion takes place for any amino acid residue. Flipbook provides an engine for transforming time-series, residue-level data into salient, colored 3D structures. Flipbook can take in RMSX values, or other user-provided values, to see how they vary with time, coloring and scaling the amino acids according to those values. We demonstrate these tools' utility on unbiased and steered MD simulations of ubiquitin, HIV-1 protease, and the bacterial adhesion protein SdrG. RMSX and Flipbook together form a streamlined, open-source suite for quantitative, high-resolution interrogation of biomolecular dynamics. RMSX and Flipbook are freely available at https://github.com/AntunesLab/rmsx .
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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.