Evidence map›Paper›PMID 40247410›Full record

ArticleJournal of cheminformatics2025

The pucke.rs toolkit to facilitate sampling the conformational space of biomolecular monomers.

Jérôme Rihon, Sten Reynders, Vitor Bernardes Pinheiro, Eveline Lescrinier

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PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of cheminformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Review
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.

Jérôme RihonLaboratory of Medicinal Chemistry, Departement of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
Sten ReyndersLaboratory of Medicinal Chemistry, Departement of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
Vitor Bernardes PinheiroLaboratory of Medicinal Chemistry, Departement of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
Eveline LescrinierLaboratory of Medicinal Chemistry, Departement of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium. eveline.lescrinier@kuleuven.be.

Funding

Research Foundation - Flanders (FWO) G085321N
6 · The paper itself

Abstract

Understanding of the structural and dynamic behaviour of molecules is a major objective in molecular modeling research. Sampling through the torsional space is an efficient way to map their behaviour. However, generating a landscape of possible conformations relies on multiple formalisms whose mathematics are often difficult to convert to code. Here we present a command line tool and a scripting module to provide the means to generate such landscapes with different axes according to various formalisms exploited for conformational sampling. Additionally to this toolkit, we apply a benchmarking study on subjecting a DNA nucleoside to a diverse set of quantum mechanical levels of theory for geometry optimisations and energy potential calculations. The potential of the tool is demonstrated on examples including amino acids and synthetic nucleosides having five-membered or six-membered sugar moieties.

Indexed as

Computational chemistryLinear algebraPuckering formalismsPythonRust

Identifiers

PMID40247410
PMCPMC12007234

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.