Evidence map›Paper›PMID 42200427›Full record

ArticleJournal of chemical theory and computation2026

Efficient QM/MM Modeling of Enzymatic Reactions Combining PathCV with OPES.

José Pablo Rivas-Fernández, Martin Calvelo, Mert Sagiroglugil, Qinghua Liao, Carme Rovira

Abstract read
In one paragraph

Article in Journal of chemical theory and computation, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0cells of the map it votes in
0citing papers in PubMed
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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

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

5 authors.

José Pablo Rivas-FernándezDepartament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.ORCID 0000-0002-1349-3049
Martin CalveloDepartament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.ORCID 0000-0001-7114-1781
Mert SagiroglugilDepartament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.ORCID 0000-0002-4714-3717
Qinghua LiaoDepartament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.ORCID 0000-0002-2260-8493
Carme RoviraDepartament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.ORCID 0000-0003-1477-5010

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations combined with enhanced sampling are powerful tools for studying enzymatic reaction mechanisms, but their application remains limited by the short time scales accessible at the QM/MM level and by the difficulty of defining efficient collective variables. Here, we present a practical protocol that combines a path collective variable (PathCV) with the exploratory variant of on-the-fly probability-enhanced sampling (OPES

Indexed as

EnzymesMolecular Dynamics SimulationQuantum MechanicsHumansSARS-CoV-2ThermodynamicsEnzymes

Identifiers

PMID42200427
PMCPMC13255176

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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.