ArticleScientific data2022
AB-DB: Force-Field parameters, MD trajectories, QM-based data, and Descriptors of Antimicrobials.
Article in Scientific data, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Substrate Specificity Checkpoints of the Multidrug Efflux Pump MexF fromACS infectious diseases · 2026Article
- Computer Simulations of Multidrug Efflux Pumps of the Resistance-Nodulation-Cell Division Superfamily.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Multitarget Neuropharmacological Actions of Drimycarpus racemosus Hook. f. GC-MS-Guided In Vivo and In Silico Evidence of Anxiolytic and Antidepressant Potential.TheScientificWorldJournal · 2026Article
- Molecular dynamics simulations of proteins: an in-depth review of computational strategies, structural insights, and their role in medicinal chemistry and drug development.Biological cybernetics · 2025Review
- Unlocking the Gates: A Novel Diagnostic Molecule for Quantifying Efflux Levels in Gram-Positive Bacteria.Advanced healthcare materials · 2025Article
- Advances in methods and concepts provide new insight into antibiotic fluxes across the bacterial membrane.Communications biology · 2024Article
- Force Fields, Quantum-Mechanical- and Molecular-Dynamics-Based Descriptors of Radiometal-Chelator Complexes.Molecules (Basel, Switzerland) · 2024Article
- Quantum mechanical electronic and geometric parameters for DNA k-mers as features for machine learning.Scientific data · 2024Article
- Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors.Communications chemistry · 2024Article
- Article
- Tripartite efflux pumps of the RND superfamily: what did we learn from computational studies?Microbiology (Reading, England) · 2023Review
- Recognition of quinolone antibiotics by the multidrug efflux transporter MexB ofPhysical chemistry chemical physics : PCCP · 2022Article
- Functional Dynamics of Substrate Recognition in TEM Beta-Lactamase.Entropy (Basel, Switzerland) · 2022Article
- AB-DB: Force-Field parameters, MD trajectories, QM-based data, and Descriptors of Antimicrobials.Scientific data · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Antibiotic resistance is a major threat to public health. The development of chemo-informatic tools to guide medicinal chemistry campaigns in the efficint design of antibacterial libraries is urgently needed. We present AB-DB, an open database of all-atom force-field parameters, molecular dynamics trajectories, quantum-mechanical properties, and curated physico-chemical descriptors of antimicrobial compounds. We considered more than 300 molecules belonging to 25 families that include the most relevant antibiotic classes in clinical use, such as β-lactams and (fluoro)quinolones, as well as inhibitors of key bacterial proteins. We provide traditional descriptors together with properties obtained with Density Functional Theory calculations. Noteworthy, AB-DB contains less conventional descriptors extracted from μs-long molecular dynamics simulations in explicit solvent. In addition, for each compound we make available force-field parameters for the major micro-species at physiological pH. With the rise of multi-drug-resistant pathogens and the consequent need for novel antibiotics, inhibitors, and drug re-purposing strategies, curated databases containing reliable and not straightforward properties facilitate the integration of data mining and statistics into the discovery of new antimicrobials.
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Registered trials
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 Socratic graph.