Evidence map›Paper›PMID 38905589›Full record

ArticleJournal of chemical theory and computation2024

k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations.

Lexin Chen, Daniel R Roe, Matthew Kochert, Carlos Simmerling, Ramón Alain Miranda-Quintana

Abstract read
In one paragraph

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 23 papers.

0numbers the graph read from it
0cells of the map it votes in
23citing 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

23 citing papers in PubMed.

  1. Article
  2. Pathway representationDigital discovery · 2026
    Article
  3. Article
  4. Article
  5. Article
  6. ScalingJournal of chemical information and modeling · 2026
    Article
  7. Article
  8. Article
  9. Beyond Classical Force Fields: Physics-Driven Assessment of the Grappa Machine-Learned Force Field on the FoldBind Dataset.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026
    Article
  10. Article
  11. Article
  12. Article
  13. Article
  14. BitBIRCH-Lean: chemical space in the palm of your workstation.bioRxiv : the preprint server for biology · 2025
    Article
  15. Article
  16. Visualization of KACS pharmacology & translational science · 2025
    Article
  17. clusttraj: A Solvent-Informed Clustering Tool for Molecular Modeling.Journal of chemical theory and computation · 2025
    Article
  18. Article
  19. Article
  20. Extended Quality (eQual): Radial Threshold Clustering Based onJournal of chemical information and modeling · 2025
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Lexin ChenDepartment of Chemistry, University of Florida, Gainesville, Florida 32611, United States.
Daniel R RoeLaboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.ORCID 0000-0002-5834-2447
Matthew KochertLaufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States.
Carlos SimmerlingDepartment of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States.ORCID 0000-0002-7252-4730
Ramón Alain Miranda-QuintanaDepartment of Chemistry, University of Florida, Gainesville, Florida 32611, United States.ORCID 0000-0003-2121-4449

Funding

New Solvent Models, Sampling Methods and Maintenance of Amber SoftwareR01GM107104 · NIGMS · STATE UNIVERSITY NEW YORK STONY BROOK · PI SIMMERLING, CARLOS · 2013 to 2020
$2.4M
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 R01 GM107104NIGMS NIH HHS R35 GM150620
6 · The paper itself

Abstract

One of the key challenges of

Identifiers

PMID38905589
PMCPMC11541788

What OpenQuestion holds

Textmetadata
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Read underepoch 390

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.