Evidence map›Paper›PMID 41218170›Full record

ArticleJournal of chemical information and modeling2026

EasyHybrid: An Interactive Graphical Environment for Quantum, Classical and Hybrid Simulations with pDynamo3.

Jose Fernando R Bachega, Gustavo Hagen, Carlos Sequeiros-Borja, Kai Nikklas, Jorge Chahine, Luis Fernando M S Timmers, Martin J Field

Abstract read
In one paragraph

Article in Journal of chemical information and modeling, 2026. 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
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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

7 authors.

Jose Fernando R BachegaDepartment of Pharmacosciences, Federal University of Health Sciences of Porto Alegre, 90050-170 Porto Alegre, RS, Brazil.ORCID 0000-0002-9849-7873
Gustavo HagenBiotechnology Center, Graduate Program in Molecular and Cellular Biology, Federal University of Rio Grande do Sul, 90650-001 Porto Alegre, RS, Brazil.ORCID 0009-0000-6525-4907
Carlos Sequeiros-BorjaTunneling Group, Biotechnology Center, Krzywoustego 8, 44-100 Gliwice, Poland.
Kai Nikklas3D Development, deCode GmbH, 46145 Oberhausen, Germany.
Jorge ChahineBiological Structures Group, Multiuser Center for Biomolecular Innovation, São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil.ORCID 0000-0002-6474-0337
Luis Fernando M S TimmersGraduate Program in Biotechnology, University of Vale do Taquari, 95900-000 Lajeado, RS, Brazil.ORCID 0000-0003-0399-5376
Martin J FieldLaboratoire de Chimie et Biologie des Métaux, UMR5249, Université Grenoble I, CEA, CNRS, 38054 Grenoble, France.ORCID 0000-0001-8674-7997

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We present EasyHybrid, a free and open-source graphical interface for hybrid quantum chemical/molecular mechanical (QC/MM) simulations built on the pDynamo3 library. The software provides an intuitive environment for preparing, inspecting, and editing molecular systems, while supporting a broad range of simulations, including reaction coordinate scans, molecular dynamics, normal-mode analysis, Nudged Elastic Band, and umbrella sampling. Key features include advanced 3D visualization of large biomolecular systems, interactive editing, flexible atom selection, system pruning for efficient QC/MM setup, orbital and electrostatic potential surfaces, automated log parsing, and trajectory analysis. EasyHybrid integrates these tools into a single platform, offering a familiar yet specialized environment for quantum chemistry and hybrid QC/MM simulations.

Indexed as

Computer GraphicsMolecular Dynamics SimulationQuantum TheorySoftwareUser-Computer Interface

Identifiers

PMID41218170
PMCPMC12892311

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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.