Evidence map›Paper›PMID 41279071›Full record

ArticlebioRxiv : the preprint server for biology2025

mdBIRCH for Fast, Scalable, Online Clustering of Molecular Dynamics Trajectories.

Jherome Brylle Woody Santos, Lexin Chen, Ramón Alain Miranda-Quintana

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

3 authors.

Jherome Brylle Woody SantosDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida, 32611, USA.
Lexin ChenDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida, 32611, USA.
Ramón Alain Miranda-QuintanaDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida, 32611, USA.ORCID 0000-0003-2121-4449

Funding

Tackling Big Data problems in biomedical sciences with extended similarity methodsR35GM150620 · NIGMS · UNIVERSITY OF FLORIDA · PI Ramon Alain Miranda Quintana · 2023 to 2026
$1.4M
NIGMS NIH HHS R35 GM150620
6 · The paper itself

Abstract

We present mdBIRCH, an online clustering method that adapts the BIRCH CF-tree to molecular dynamics (MD) data by using a merge test calibrated directly to RMSD. Each arriving frame is routed to the nearest centroid and added only if the post-merge radius computed from the cluster feature remains within a user-supplied threshold. This keeps the average deviation to each cluster centroid bounded as the cluster grows and preserves a simple interpretation of resolution in physical units. We evaluate mdBIRCH on a

Identifiers

PMID41279071
PMCPMC12637632

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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Registered trials

None linked

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.