ArticleMolecules (Basel, Switzerland)2015
A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds.
Article in Molecules (Basel, Switzerland), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Computer Simulations of Multidrug Efflux Pumps of the Resistance-Nodulation-Cell Division Superfamily.Methods in molecular biology (Clifton, N.J.) · 2026Article
- 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
- Property space mapping of Pseudomonas aeruginosa permeability to small molecules.Scientific reports · 2022Article
- AB-DB: Force-Field parameters, MD trajectories, QM-based data, and Descriptors of Antimicrobials.Scientific data · 2022Article
- Pyridylpiperazine-based allosteric inhibitors of RND-type multidrug efflux pumps.Nature communications · 2022Article
- Structural and functional analysis of the promiscuous AcrB and AdeB efflux pumps suggests different drug binding mechanisms.Nature communications · 2021Article
- The Whole Is Bigger than the Sum of Its Parts: Drug Transport in the Context of Two Membranes with Active Efflux.Chemical reviews · 2021Article
- Article
- Permeation of β-Lactamase Inhibitors through the General Porins of Gram-Negative Bacteria.Molecules (Basel, Switzerland) · 2020Article
- Perturbed structural dynamics underlie inhibition and altered efflux of the multidrug resistance pump AcrB.Nature communications · 2020Article
- Chlorpromazine and Amitriptyline Are Substrates and Inhibitors of the AcrB Multidrug Efflux Pump.mBio · 2020Article
- The challenge of intracellular antibiotic accumulation, a function of fluoroquinolone influx versus bacterial efflux.Communications biology · 2020Article
- Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB.Journal of molecular biology · 2020Article
- Molecular Interactions of Carbapenem Antibiotics with the Multidrug Efflux Transporter AcrB ofInternational journal of molecular sciences · 2020Article
- Molecular Interactions of Cephalosporins with the Deep Binding Pocket of the RND Transporter AcrB.The journal of physical chemistry. B · 2019Article
- Ampicillin permeation across OmpF, the major outer-membrane channel inThe Journal of biological chemistry · 2018Article
- Molecular Determinants of the Promiscuity of MexB and MexY Multidrug Transporters ofFrontiers in microbiology · 2018Article
- MOMP from Campylobacter jejuni Is a Trimer of 18-Stranded β-Barrel Monomers with a CaJournal of molecular biology · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present an on-line database of all-atom force-field parameters and molecular properties of compounds with antimicrobial activity (mostly antibiotics and some beta-lactamase inhibitors). For each compound, we provide the General Amber Force Field parameters for the major species at physiological pH, together with an analysis of properties of interest as extracted from µs-long molecular dynamics simulations in explicit water solution. The properties include number and population of structural clusters, molecular flexibility, hydrophobic and hydrophilic molecular surfaces, the statistics of intraand inter-molecular H-bonds, as well as structural and dynamical properties of solvent molecules within first and second solvation shells. In addition, the database contains several key molecular parameters, such as energy of the frontier molecular orbitals, vibrational properties, rotational constants, atomic partial charges and electric dipole moment, computed by Density Functional Theory. The present database (to our knowledge the first extensive one including dynamical properties) is part of a wider project aiming to build-up a database containing structural, physico-chemical and dynamical properties of medicinal compounds using different force-field parameters with increasing level of complexity and reliability. The database is freely accessible at http://www.dsf.unica.it/translocation/db/.
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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 OpenQuestion graph.