ArticleJournal of chemical theory and computation2024
Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- Pathway representationDigital discovery · 2026Article
- Temperature-Dependent Thumb Domain Dynamics of Xylanase TsaGH11: Insights from Molecular Dynamics Simulations.International journal of molecular sciences · 2026Article
- Pathway Representation via Intrinsic Structural Medoids (PRISM): A Structural Mapping Approach to Clustering Molecular Pathways.bioRxiv : the preprint server for biology · 2026Article
- mdBIRCH for Fast, Scalable, Online Clustering of Molecular Dynamics Trajectories.Journal of chemical theory and computation · 2026Article
- Divide and Cluster: The DIVINE Framework for Deterministic Top-Down Analysis of Molecular Dynamics Trajectories.Journal of chemical information and modeling · 2026Article
- Selector: A General Python Library for Diverse Subset Selection.Journal of chemical information and modeling · 2026Article
- Selector: A General Python Library for Diverse Subset Selection.bioRxiv : the preprint server for biology · 2025Article
- mdBIRCH for Fast, Scalable, Online Clustering of Molecular Dynamics Trajectories.bioRxiv : the preprint server for biology · 2025Article
- clusttraj: A Solvent-Informed Clustering Tool for Molecular Modeling.Journal of chemical theory and computation · 2025Article
- CADENCE: Clustering Algorithm─Density-Based Exploration and Novelty Clustering with Efficiency.Journal of chemical information and modeling · 2025Article
- Hierarchical Extended Linkage Method (HELM)'s Deep Dive into Hybrid Clustering Strategies.Journal of chemical information and modeling · 2025Article
- Extended Quality (eQual): Radial Threshold Clustering Based onJournal of chemical information and modeling · 2025Article
- SHINE: Deterministic Many-to-Many Clustering of Molecular Pathways.Journal of chemical information and modeling · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Molecular dynamics (MD) simulations are ideally suited to describe conformational ensembles of biomolecules such as proteins and nucleic acids. Microsecond-long simulations are now routine, facilitated by the emergence of graphical processing units. Clustering, which groups objects based on structural similarity, is typically used to process ensembles, leading to different states, their populations, and the identification of representative structures. A popular pipeline combines hierarchical clustering for clustering and selecting the cluster centroid as representative of the cluster. Here, we propose to improve on this approach, by developing a module-Protein Retrieval via Integrative Molecular Ensembles (PRIME), that consists of tools to improve the prediction of the representative in the most populated cluster using extended continuous similarity. PRIME is integrated with our Molecular Dynamics Analysis with
Indexed as
Identifiers
What OpenQuestion holds
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.