title: A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds.
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/.
authors.affiliation: Dipartimento di Fisica, Università degli studi di Cagliari, Cittadella Universitaria, I-09042 Monserrato (Cagliari), Italy. giuliano.malloci@dsf.unica.it.
authors.forename: Giuliano
authors.initials: G
authors.lastname: Malloci
authors.affiliation: Dipartimento di Fisica, Università degli studi di Cagliari, Cittadella Universitaria, I-09042 Monserrato (Cagliari), Italy. vargiu@dsf.unica.it.
authors.forename: Attilio Vittorio
authors.initials: AV
authors.lastname: Vargiu
authors.affiliation: Dipartimento di Fisica, Università degli studi di Cagliari, Cittadella Universitaria, I-09042 Monserrato (Cagliari), Italy. gserra@dsf.unica.it.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Serra
authors.affiliation: Dipartimento di Fisica, Università degli studi di Cagliari, Cittadella Universitaria, I-09042 Monserrato (Cagliari), Italy. andrea.bosin@dsf.unica.it.
authors.forename: Andrea
authors.initials: A
authors.lastname: Bosin
authors.affiliation: Dipartimento di Fisica, Università degli studi di Cagliari, Cittadella Universitaria, I-09042 Monserrato (Cagliari), Italy. paolo.ruggerone@dsf.unica.it.
authors.forename: Paolo
authors.initials: P
authors.lastname: Ruggerone
authors.affiliation: Dipartimento di Fisica, Università degli studi di Cagliari, Cittadella Universitaria, I-09042 Monserrato (Cagliari), Italy. matteo.ceccarelli@dsf.unica.it.
authors.forename: Matteo
authors.initials: M
authors.lastname: Ceccarelli
mesh_terms: D000890:Anti-Infective Agents / Q000494:pharmacology*; D062126:Databases, Chemical; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D000890:Anti-Infective Agents
keywords: all-atom force fields; antimicrobial compounds; molecular databases; molecular dynamics simulations