AB-DB v2.0: an integrated chemoinformatic resource for antimicrobial compounds
Abstract
Antibiotic resistance is a major threat to public health and calls for chemoinformatic tools that can help the design of antibacterial discovery libraries. We present AB-DB v2.0, a freely available online database of molecular dynamics (MD) trajectories, quantum-mechanical (QM) simulations, force field parameters, and curated physico-chemical descriptors of antimicrobial compounds. AB-DB v2.0 is fully integrated into the Molecular Dynamics Data Bank (MDDB), which provides an interactive web-based environment for visualization, exploration, and on-the-fly analysis of trajectories. QM simulations are included in the ioChem-BD platform, providing a distributed and provenance-tracked repository for computational chemistry results. The database contains more than 470 molecules belonging to 51 antimicrobial classes, including the most relevant families in clinical use, such as β β -lactams and quinolones, as well as inhibitors of key bacterial targets and peptide-based agents. Force field parameters and molecular descriptors are available for the major micro-species at physiological pH, ensuring direct reusability in MD, docking, modelling, and machine-learning workflows.
Scientific Contribution
By integrating MD trajectories, QM simulations, force field parameters, and curated physico-chemical descriptors in a single and inter-connected resource, AB-DB v2.0 provides a unique multidimensional framework for antimicrobial data analysis and discovery. This combination enables direct reusability in MD, docking, modelling, and machine-learning workflows.
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BibTeX
@article{gervasoni2026abdb,
title = {{AB-DB v2.0: an integrated chemoinformatic resource for antimicrobial compounds}},
author = {Silvia Gervasoni and Genís Bayarri and Andrea Bosin and Attilio V. Vargiu and Modesto Orozco and Adam Hospital and Giuliano Malloci},
journal = {Journal of Cheminformatics},
year = {2026},
month = oct,
doi = {10.1186/s13321-026-01314-2},
url = {https://link.springer.com/article/10.1186/s13321-026-01314-2},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - AB-DB v2.0: an integrated chemoinformatic resource for antimicrobial compounds
AU - Silvia Gervasoni
AU - Genís Bayarri
AU - Andrea Bosin
AU - Attilio V. Vargiu
AU - Modesto Orozco
AU - Adam Hospital
AU - Giuliano Malloci
PY - 2026
DA - 2026/10/20
JO - Journal of Cheminformatics
DO - 10.1186/s13321-026-01314-2
UR - https://link.springer.com/article/10.1186/s13321-026-01314-2
AB - Antibiotic resistance is a major threat to public health and calls for chemoinformatic tools that can help the design of antibacterial discovery libraries. We present AB-DB v2.0, a freely available online database of molecular dynamics (MD) trajectories, quantum-mechanical (QM) simulations, force field parameters, and curated physico-chemical descriptors of antimicrobial compounds. AB-DB v2.0 is fully integrated into the Molecular Dynamics Data Bank (MDDB), which provides an interactive web-based environment for visualization, exploration, and on-the-fly analysis of trajectories. QM simulations are included in the ioChem-BD platform, providing a distributed and provenance-tracked repository for computational chemistry results. The database contains more than 470 molecules belonging to 51 antimicrobial classes, including the most relevant families in clinical use, such as β β -lactams and quinolones, as well as inhibitors of key bacterial targets and peptide-based agents. Force field parameters and molecular descriptors are available for the major micro-species at physiological pH, ensuring direct reusability in MD, docking, modelling, and machine-learning workflows. Scientific Contribution By integrating MD trajectories, QM simulations, force field parameters, and curated physico-chemical descriptors in a single and inter-connected resource, AB-DB v2.0 provides a unique multidimensional framework for antimicrobial data analysis and discovery. This combination enables direct reusability in MD, docking, modelling, and machine-learning workflows.
SN - 1758-2946
ER -