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Molecules 2015, 20(8), 13997-14021; doi:10.3390/molecules200813997

A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds

Dipartimento di Fisica, Università degli studi di Cagliari, Cittadella Universitaria, I-09042 Monserrato (Cagliari), Italy
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Author to whom correspondence should be addressed.
Academic Editor: Peter Ertl
Received: 11 June 2015 / Accepted: 28 July 2015 / Published: 3 August 2015
(This article belongs to the Special Issue Chemoinformatics)
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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/. View Full-Text
Keywords: antimicrobial compounds; molecular databases; all-atom force fields; molecular dynamics simulations antimicrobial compounds; molecular databases; all-atom force fields; molecular dynamics simulations
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Malloci, G.; Vargiu, A.V.; Serra, G.; Bosin, A.; Ruggerone, P.; Ceccarelli, M. A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds. Molecules 2015, 20, 13997-14021.

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