Cargando…

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

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 p...

Descripción completa

Detalles Bibliográficos
Autores principales:	Malloci, Giuliano, Vargiu, Attilio Vittorio, Serra, Giovanni, Bosin, Andrea, Ruggerone, Paolo, Ceccarelli, Matteo
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	MDPI 2015
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6332394/ https://www.ncbi.nlm.nih.gov/pubmed/26247924 http://dx.doi.org/10.3390/molecules200813997

Ejemplares similares

AB-DB: Force-Field parameters, MD trajectories, QM-based data, and Descriptors of Antimicrobials
por: Gervasoni, Silvia, et al.
Publicado: (2022)

Molecular Interactions of Carbapenem Antibiotics with the Multidrug Efflux Transporter AcrB of Escherichia coli
por: Atzori, Alessio, et al.
Publicado: (2020)

Common recognition topology of mex transporters of Pseudomonas aeruginosa revealed by molecular modelling
por: Catte, Andrea, et al.
Publicado: (2022)

Recognition of quinolone antibiotics by the multidrug efflux transporter MexB of Pseudomonas aeruginosa
por: Gervasoni, Silvia, et al.
Publicado: (2022)

Tripartite efflux pumps of the RND superfamily: what did we learn from computational studies?
por: Athar, Mohd, et al.
Publicado: (2023)

Molecular Determinants of the Promiscuity of MexB and MexY Multidrug Transporters of Pseudomonas aeruginosa
por: Ramaswamy, Venkata K., et al.
Publicado: (2018)

Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters
por: Ramaswamy, Venkata Krishnan, et al.
Publicado: (2017)

Interaction of Radiopharmaceuticals with Somatostatin Receptor 2 Revealed by Molecular Dynamics Simulations
por: Gervasoni, Silvia, et al.
Publicado: (2023)

Molecular rationale for the impairment of the MexAB-OprM efflux pump by a single mutation in MexA
por: Cacciotto, Pierpaolo, et al.
Publicado: (2021)

A framework for dissecting affinities of multidrug efflux transporter AcrB to fluoroquinolones
por: Vergalli, Julia, et al.
Publicado: (2022)

Molecular determinants of avoidance and inhibition of Pseudomonas aeruginosa MexB efflux pump
por: Gervasoni, Silvia, et al.
Publicado: (2023)

Molecular simulations of SSTR2 dynamics and interaction with ligands
por: Gervasoni, Silvia, et al.
Publicado: (2023)

The challenge of intracellular antibiotic accumulation, a function of fluoroquinolone influx versus bacterial efflux
por: Vergalli, Julia, et al.
Publicado: (2020)

Dissociation of minor groove binders from DNA: insights from metadynamics simulations
por: Vargiu, Attilio Vittorio, et al.
Publicado: (2008)

Time-Dependent Density Functional Theory Investigation on the Electronic and Optical Properties of Poly-C,Si,Ge-acenes
por: Mocci, Paola, et al.
Publicado: (2020)

Chlorpromazine and Amitriptyline Are Substrates and Inhibitors of the AcrB Multidrug Efflux Pump
por: Grimsey, Elizabeth M., et al.
Publicado: (2020)

Computational Study of Correlated Domain Motions in the AcrB Efflux Transporter
por: Schulz, Robert, et al.
Publicado: (2015)

Exploring Binding Properties of Agonists Interacting with a δ-Opioid Receptor
por: Collu, Francesca, et al.
Publicado: (2012)

Functional Rotation of the Transporter AcrB: Insights into Drug Extrusion from Simulations
por: Schulz, Robert, et al.
Publicado: (2010)

Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps
por: Ruggerone, Paolo, et al.
Publicado: (2013)

Perturbed structural dynamics underlie inhibition and altered efflux of the multidrug resistance pump AcrB
por: Reading, Eamonn, et al.
Publicado: (2020)

Structural and functional analysis of the promiscuous AcrB and AdeB efflux pumps suggests different drug binding mechanisms
por: Ornik-Cha, Alina, et al.
Publicado: (2021)

Improving Small-Molecule Force Field Parameters in Ligand Binding Studies
por: Raniolo, Stefano, et al.
Publicado: (2021)

Interaction of antibacterial compounds with RND eﬄux pumps in Pseudomonas aeruginosa
por: Dreier, Jürg, et al.
Publicado: (2015)

Molecular Insights Into Binding and Activation of the Human KCNQ2 Channel by Retigabine
por: Garofalo, Barbara, et al.
Publicado: (2022)

Electronic and Optical Properties of Small Metal Fluoride Clusters
por: Cappellini, Giancarlo, et al.
Publicado: (2020)

Relevance of Ebola virus VP35 homo-dimerization on the type I interferon cascade inhibition
por: Di Palma, Francesco, et al.
Publicado: (2019)

HIV-1 Protease Dimerization Dynamics Reveals a Transient Druggable Binding Pocket at the Interface
por: Pietrucci, Fabio, et al.
Publicado: (2015)

Predictive Rules of Efflux Inhibition and Avoidance in Pseudomonas aeruginosa
por: Mehla, Jitender, et al.
Publicado: (2021)

Assessment of Lipophilicity Parameters of Antimicrobial and Immunosuppressive Compounds
por: Wardecki, Dawid, et al.
Publicado: (2023)

The Alexandria library, a quantum-chemical database of molecular properties for force field development
por: Ghahremanpour, Mohammad M., et al.
Publicado: (2018)

Robust AMBER Force Field Parameters for Glutathionylated Cysteines
por: Elftmaoui, Zineb, et al.
Publicado: (2023)

The Structural and Functional Study of Efflux Pumps Belonging to the RND Transporters Family from Gram-Negative Bacteria
por: Vargiu, Attilio Vittorio, et al.
Publicado: (2022)

Permeation of β-Lactamase Inhibitors through the General Porins of Gram-Negative Bacteria
por: Pira, Alessandro, et al.
Publicado: (2020)

MIC database: A collection of antimicrobial compounds from literature
por: Babu, Padavala Ajay, et al.
Publicado: (2009)

Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue
por: Jandova, Zuzana, et al.
Publicado: (2021)

Optimization of Slipids Force Field Parameters Describing Headgroups of Phospholipids
por: Grote, Fredrik, et al.
Publicado: (2020)

Development and Testing of Force Field Parameters for Phenylalanine and Tyrosine Derivatives
por: Wang, Xiaowen, et al.
Publicado: (2020)

Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness
por: Conflitti, Paolo, et al.
Publicado: (2023)

Dataset of molecular dynamics simulation trajectories of amino-acid solutions with various force fields, water models and modified force field parameters
por: Průša, Jiří, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_0gho24c6l1rlo82sg5g4b97lcq