Evidence map›Paper›PMID 38261112›Full record

ArticleJournal of molecular modeling2024

Optimization of CHARMM force field parameters for ryanodine receptor inhibitory drug dantrolene using FFTK and FFParam.

Saliha Nur Uludag, Cemil Can Saylan, Adem Tekin, Sefer Baday

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In one paragraph

Article in Journal of molecular modeling, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.7field-weighted citation impact, top 33% of its field
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

1 citing paper in PubMed, 3 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors at 3 institutions in 2 countries.

Saliha Nur UludagComputational Science and Engineering Department, Informatics Institute, Istanbul Technical University, Ayazaga Campus, Maslak, 34469, Istanbul, Türkiye.
Cemil Can SaylanComputational Science and Engineering Department, Informatics Institute, Istanbul Technical University, Ayazaga Campus, Maslak, 34469, Istanbul, Türkiye.
Adem TekinComputational Science and Engineering Department, Informatics Institute, Istanbul Technical University, Ayazaga Campus, Maslak, 34469, Istanbul, Türkiye.
Sefer BadayComputational Science and Engineering Department, Informatics Institute, Istanbul Technical University, Ayazaga Campus, Maslak, 34469, Istanbul, Türkiye. badays@itu.edu.tr.
Istanbul Technical University · TRScientific and Technological Research Council of Turkey · TRTechnical University of Munich · DE

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

contextRyanodine receptors (RyRs) are large intracellular ligand-gated calcium release ion channels. Mutations in human RyR1 in combination with a volatile anesthetic or muscle relaxant are known to cause leaky RyRs resulting in malignant hyperthermia (MH). This has long been primarily treated with the RyR inhibitory drug dantrolene. Alternatives to dantrolene as a RyR inhibitor may be found through computer-aided drug design. Additionally, molecular dynamics (MD) studies of dantrolene interacting with RyRs may reveal its full mechanism of action. The availability of accurate force field parameters is important for the success of both.

methodsIn this study, force field parameters for dantrolene were obtained from the CHARMM General Force Field (CGenFF) program and optimized using the force field toolkit (FFTK) and FFParam programs. The obtained parameters were then validated by a comparison between calculated and experimental IR spectra and normal mode analysis, among other techniques.

Indexed as

DantroleneRyanodine Receptor Calcium Release ChannelCalciumDrug DesignHumansMutationCalciumDantroleneRyanodine Receptor Calcium Release ChannelDantroleneFFParamFFTKForce fieldRyanodine receptor

Identifiers

PMID38261112
OpenAlexW4391137533

What OpenQuestion holds

Textmetadata
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.