L. Bonati

发表

Computational approaches to shed light on molecular mechanisms in biological processes

E. Papaleo, G. Moro, A. Pandini, 2007, Theoretical chemistry accounts.

Giancarlo Mauri, Alessandro Pandini, Annalisa Bordogna, 2007, Protein engineering, design & selection : PEDS.

Trends in Ecological Physical Chemistry.

Marina Lasagni, Laura Bonati, Demetrio Pitea, 1994 .

Identification of potential aryl hydrocarbon receptor ligands by virtual screening of industrial chemicals

C. D. Andersson, A. Linusson, P. Andersson, 2017, Environmental Science and Pollution Research.

Defining the limits of homology modeling in information‐driven protein docking

A. Bordogna, E. Karaca, P. Kastritis, 2013, Proteins.

The combustion of municipal solid wastes and PCDD and PCDF emissions. Part 1. PCDD and PCDF in MSW

R. Todeschini, G. Moro, M. Lasagni, 1989 .

Conservation and specialization in PAS domain dynamics.

A Pandini, A. Pandini, L. Bonati, 2005, Protein engineering, design & selection : PEDS.

Exploring the PXR ligand binding mechanism with advanced Molecular Dynamics methods

L. Callea, L. Bonati, S. Motta, 2018, Scientific Reports.

Ginsenosides Are Novel Naturally-Occurring Aryl Hydrocarbon Receptor Ligands

M. Denison, Bin Zhao, A. Zhang, 2013, PloS one.

Comparative In Vitro and In Silico Analysis of the Selectivity of Indirubin as a Human Ah Receptor Agonist

M. Denison, L. Bonati, Sara Giani Tagliabue, 2018, International journal of molecular sciences.

AHR Ligands: Promiscuity in Binding and Diversity in Response

M. Denison, G. He, L. Bonati, 2011 .

3D QSAR The Integration of QSAR with Molecular Modeling

Roberto Todeschini, Gabriele Cruciani, Laura Bonati, 1994 .

A comparative analysis of molecular electrostatic potentials of chlorinated dibenzo-p-dioxins in relation to their biological activity

M. Lasagni, D. Pitea, L. Bonati, 1991 .

Comparative Analysis of Homology Models of the Ah Receptor Ligand Binding Domain: Verification of Structure-function Predictions by Site-directed Mutagenesis of a Non-functional Ahr † Nih Public Access

A. Pandini, M. E. Hahn, S. Karchner, 2022 .

On the role of the molecular electrostatic potential in modelling the activity of non-peptide angiotensin II receptor antagonists

Anna Vulpetti, Carlo Scolastico, Gianpaolo Bravi, 1993 .

The Role of the Molecular Electrostatic Potential in Modeling the Activity of Non-Peptide Angiotensin II Receptor Antagonists

G. Bravi, L. Belvisi, A. Vulpetti, 1993 .

A hypothesis on the mechanism of PCDD biological activity based on molecular electrostatic potential modeling. Part 2

M. Lasagni, D. Pitea, L. Bonati, 1995 .

Modeling the binding of diverse ligands within the Ah receptor ligand binding domain

M. Denison, L. Bonati, S. Motta, 2019, Scientific Reports.

An Aryl Hydrocarbon Receptor from the Caecilian Gymnopis multiplicata Suggests Low Dioxin Affinity in the Ancestor of All Three Amphibian Orders.

M. E. Hahn, M. Denison, D. G. Franks, 2020, General and comparative endocrinology.

Specific ligand binding domain residues confer low dioxin responsiveness to AHR1β of Xenopus laevis.

M. E. Hahn, M. Denison, D. G. Franks, 2013, Biochemistry.

In vitro toxicity and in silico docking analysis of two novel selective AH-receptor modulators.

R. Pohjanvirta, L. Bonati, A. Nasri, 2018, Toxicology in vitro : an international journal published in association with BIBRA.

The Cellular and Molecular Determinants of Naphthoquinone-Dependent Activation of the Aryl Hydrocarbon Receptor

M. Denison, L. Bonati, Sara Giani Tagliabue, 2020, International journal of molecular sciences.

Transitional States in Ligand-Dependent Transformation of the Aryl Hydrocarbon Receptor into Its DNA-Binding Form

M. Denison, L. Bonati, S. Motta, 2020, International journal of molecular sciences.

Molecular Polarizability as a Tool for Understanding the Binding Properties of Polychlorinated Dibenzo-p-dioxins: Definition of a Reliable Computational Procedure.

D. Pitea, L. Bonati, E. Fraschini, 1996 .

Computational prediction and in vitro validation of VEGFR1 as a novel protein target for 2,3,7,8-tetrachlorodibenzo-p-dioxin

M. Nagarkatti, P. Nagarkatti, Xiaoming Yang, 2019, Scientific Reports.

Rate enhancement of 1,3-dipolar cycloaddition of N-methylindole: the singular role of Grignard reagents

S. Grandi, D. Pitea, T. Benincori, 1998 .

An Aryl Hydrocarbon Receptor from the Caecilian Gymnopis multiplicata Suggests Low Dioxin Affinity in the Ancestor of All Three Amphibian Orders

M. E. Hahn, M. Denison, D. G. Franks, 2019, bioRxiv.

On the choice of the perturbed state for pmo prediction of selectivities in cycloaddition reactions

G. Moro, D. Pitea, L. Bonati, 1990 .

Design of gliadin peptide analogues with low affinity for the celiac disease associated HLA-DQ2 protein.

L. Bonati, Domenico Fraccalvieri, S. Motta, 2014, Molecular bioSystems.

Title Ligand binding and activation of the Ah receptor Permalink

A. Pandini, E. Baldwin, L. Bonati, 2008 .

Ligand binding and activation of the Ah receptor.

Alessandro Pandini, Laura Bonati, A. Pandini, 2002, Chemico-biological interactions.

Intermolecular interactions that determine the regioselectivity in 1,3-dipolar cycloadditions of N-methyl-1,3-oxazolium-5-olates with N-(phenylmethylene)benzenesulphonamide

L. Bonati, R. Ferraccioli, G. Moro, 1995 .

Extension of a perturbation molecular orbitals model to the study of regioselectivity in 1,3-dipolar cycloadditions: reactions of 3,5-dichloro-2,4,6-trimethylbenzonitrile oxide with heteroaromatic systems

D. Pitea, T. Benincori, L. Bonati, 1991 .

A model for recognition of polychlorinated dibenzo-p-dioxins by the aryl hydrocarbon receptor.

A Tramontano, A. Tramontano, D. Pitea, 2002, European journal of biochemistry.

Modeling the binding of diverse ligands within the Ah receptor ligand binding domain

M. Denison, L. Bonati, S. Motta, 2019, Scientific reports.

Aryl Hydrocarbon Receptor-Dependent and -Independent Pathways Mediate Curcumin Anti-Aging Effects

X. Coumoul, C. Esser, N. Ventura, 2022, bioRxiv.

Aryl hydrocarbon receptor-dependent and -independent pathways 1 mediate curcumin anti-aging effects 2

X. Coumoul, C. Esser, N. Ventura, 2022 .

Predicting the accuracy of protein–ligand docking on homology models

Alessandro Pandini, Annalisa Bordogna, Laura Bonati, 2011, J. Comput. Chem..

Exploring the PXR ligand binding mechanism with advanced Molecular Dynamics methods

L. Callea, L. Bonati, S. Motta, 2018, Scientific Reports.

Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation

Laura Bonati, Dario Corrada, Anatoly A. Soshilov, 2016, PLoS Comput. Biol..

Structural modeling of the AhR:ARNT complex in the bHLH-PASA-PASB region elucidates the key determinants of dimerization.

Laura Bonati, Dario Corrada, D. Corrada, 2017, Molecular bioSystems.

An Aryl Hydrocarbon Receptor from the Salamander Ambystoma mexicanum Exhibits Low Sensitivity to 2,3,7,8-Tetrachlorodibenzo-p-dioxin.

M. E. Hahn, M. Denison, D. G. Franks, 2015, Environmental science & technology.

New Aryl Hydrocarbon Receptor Homology Model Targeted To Improve Docking Reliability

Annalisa Bordogna, Laura Bonati, Ilaria Motto, 2011, J. Chem. Inf. Model..

Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis.

Alessandro Pandini, Jing Zhao, Laura Bonati, 2009, Biochemistry.

Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis.

Alessandro Pandini, Laura Bonati, A. Pandini, 2007, Biochemistry.

PathDetect-SOM: A Neural Network Approach for the Identification of Pathways in Ligand Binding Simulations

A. Pandini, L. Callea, L. Bonati, 2022, Journal of chemical theory and computation.

Ligand-induced perturbation of the HIF-2α:ARNT dimer dynamics

Alessandro Pandini, Laura Bonati, Stefano Motta, 2018, PLoS Comput. Biol..

Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms.

Laura Bonati, Stefano Motta, Dario Corrada, 2017, Current opinion in toxicology.

Toward a mechanistic understanding of PCDD biological activity based on molecular electrostatic potential modeling

M. Lasagni, D. Pitea, L. Bonati, 1994 .

Modeling and prediction of molecular properties. Theory of grid-weighted holistic invariant molecular (G-WHIM) descriptors

Marina Lasagni, Roberto Todeschini, Laura Bonati, 1997 .

Computational prediction and in vitro validation of VEGFR1 as a novel protein target for 2,3,7,8-tetrachlorodibenzo-p-dioxin

M. Nagarkatti, P. Nagarkatti, Xiaoming Yang, 2019, Scientific Reports.

Docking to homology models highlights the molecular determinants of ligand binding to the AhR

L. Bonati, S. G. Tagliabue, 2017, ISMB/ECCB 2017.

Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations

P. Carloni, Bharath Raghavan, E. Ippoliti, 2023, J. Chem. Inf. Model..

Evidence that ligand binding is a key determinant of Ah receptor-mediated transcriptional activity.

Laura Bonati, Jeffrey M Peters, J. Peters, 2005, Archives of biochemistry and biophysics.

Molecular electrostatic potential of substituted aromatic compounds: Factors affecting the differences between Ab Initio and semiempirical results

Laura Bonati, Ugo Cosentino, Demetrio Pitea, 1992 .

Functional annotation of the mesophilic-like character of mutants in a cold-adapted enzyme by self-organising map analysis of their molecular dynamics.

Alessandro Pandini, Matteo Tiberti, Elena Papaleo, 2012, Molecular bioSystems.

Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches

Laura Bonati, Stefano Motta, L. Bonati, 2017, J. Chem. Inf. Model..

Estimation of the toxicity equivalents of PCDD/PCDF mixtures from combustion sources when specific congener information is lacking: Preliminary results

M. Lasagni, D. Pitea, L. Bonati, 1993 .

The Toxicity Equivalency Factor Scheme Applied To Municipal Incinerator Pcdd/Pcdf Emissions When Specific Congener Information Is Lacking

M. Lasagni, D. Pitea, L. Bonati, 1992 .

Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

Fabio Stella, Alessandro Pandini, Laura Bonati, 2011, BMC Bioinformatics.

Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks

A. Pandini, A. Fornili, L. Bonati, 2021, Journal of chemical theory and computation.

Comparative analysis of homology models of the AH receptor ligand binding domain: verification of structure-function predictions by site-directed mutagenesis of a nonfunctional receptor.

A. Pandini, M. E. Hahn, S. Karchner, 2013, Biochemistry.

Self Organizing Maps to efficiently cluster and functionally interpret protein conformational ensembles

Fabio Stella, Laura Bonati, Domenico Fraccalvieri, 2013, WIVACE.

Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis.

A. Pandini, M. Denison, Jing Zhao, 2009, Biochemistry.

NURA: A curated dataset of nuclear receptor modulators.

Davide Ballabio, Francesca Grisoni, Laura Bonati, 2020, Toxicology and applied pharmacology.

States in Ligand-Dependent Transformation of the Aryl Receptor into Its DNA-Binding Form.

M. Denison, L. Bonati, S. Motta, 2020 .

The AhR signaling mechanism: a structural point of view.

L. Callea, L. Bonati, S. Motta, 2023, Journal of molecular biology.

TCDD-Induced Allosteric Perturbation of the AhR:ARNT Binding to DNA

L. Bonati, S. Motta, 2023, International journal of molecular sciences.

Specific ligand binding domain residues confer low dioxin responsiveness to AHR1β of Xenopus laevis.

M. E. Hahn, M. Denison, D. G. Franks, 2013, Biochemistry.

Testing structure-binding predictions from comparative modeling of the AHR ligand-binding domain: Studies with zebrafish AHR1a

A. Pandini, M. E. Hahn, S. Karchner, 2011 .

Computational prediction and in vitro validation of VEGFR1 as a novel protein target for 2,3,7,8-tetrachlorodibenzo-p-dioxin

M. Nagarkatti, P. Nagarkatti, Xiaoming Yang, 2019, Scientific Reports.