Paolo Carloni

发表

Supraligand fine tuning of Zn-based enzymes: the case of Horse Liver alcohol dehydrogenase

Francesco Luigi Gervasio, Michele Parrinello, Schettino, 2001 .

On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions

Paolo Carloni, Roberto Marchese, Rita Grandori, 2010, PLoS Comput. Biol..

On the active site of mononuclear B1 metallo β-lactamases: a computational study

Alessandra Magistrato, Matteo Dal Peraro, Paolo Carloni, 2012, Journal of Computer-Aided Molecular Design.

On the nature of the reaction intermediate in the HIV-1 protease: a quantum chemical study

Paolo Carloni, Simone Raugei, V. Carnevale, 2008, Comput. Phys. Commun..

Structural prediction of the interaction of the tumor suppressor p27KIP1 with cyclin A/CDK2 identifies a novel catalytically relevant determinant

Jinyu Li, Paolo Carloni, Jörg Vervoorts, 2017, BMC Bioinformatics.

Parameterization of azole‐bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure

Alessandra Magistrato, Ursula Rothlisberger, Jan Reedijk, 2008, J. Comput. Chem..

Hybrid Car-Parrinello Molecular Dynamics/Molecular Mechanics Simulations: a Powerful Tool for the Investigation of Biological Systems

Ursula Rothlisberger, Emiliano Ippoliti, Paolo Carloni, 2012 .

Chemosensorial G-proteins-coupled receptors: a perspective from computational methods.

Paolo Carloni, Alejandro Giorgetti, Francesco Musiani, 2014, Advances in experimental medicine and biology.

Topologically Based Multipolar Reconstruction of Electrostatic Interactions in Multiscale Simulations of Proteins.

Michele Cascella, Matteo Dal Peraro, Paolo Carloni, 2008, Journal of chemical theory and computation.

MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry.

Ursula Rothlisberger, Paolo Carloni, Simone Meloni, 2019, Journal of chemical theory and computation.

Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-Based Hybrid Molecular Mechanics/Coarse-Grained Approach

Ksenia Korshunova, Paolo Carloni, Alejandro Giorgetti, 2020, J. Chem. Inf. Model..

Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer

Jinyu Li, Paolo Carloni, Simone Raugei, 2014, PLoS Comput. Biol..

Promoting transparency and reproducibility in enhanced molecular simulations

Jakub Rydzewski, Toni Giorgino, Massimiliano Bonomi, 2019, Nature Methods.

RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations.

Giovanni Bussi, Gabriele Varani, Paolo Carloni, 2013, Journal of chemical theory and computation.

Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals

Ursula Rothlisberger, Rebecca C. Wade, Daniel Trpevski, 2019, bioRxiv.

Extreme Scalability of DFT-based QM/MM MD Simulations Using MiMiC.

Ursula Rothlisberger, Martin Peter Bircher, Paolo Carloni, 2019, Journal of chemical theory and computation.

Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations.

Ksenia Korshunova, Paolo Carloni, Alejandro Giorgetti, 2018, Biochemical and biophysical research communications.

Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations

Paolo Carloni, Gianluca Lattanzi, Carla Molteni, 2009, PLoS Comput. Biol..

Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study

Gabriele Varani, Paolo Carloni, Fan Yang, 2018, PLoS Comput. Biol..

Molecular motions in drug design: the coming age of the metadynamics method

Xevi Biarnés, Paolo Carloni, Paolo Ruggerone, 2011, J. Comput. Aided Mol. Des..

Unifying view of mechanical and functional hotspots across class A GPCRs

Luca Ponzoni, Cristian Micheletti, Paolo Carloni, 2017, PLoS Comput. Biol..

Structural models of human big conductance calcium- and voltage-gated potassium channels

Frank E. Blaney, Paolo Carloni, Claudio Anselmi, 2007, Comput. Phys. Commun..

Molecular Mechanics/Coarse-Grained Models

Paolo Carloni, Alejandro Giorgetti, P. Carloni, 2014 .

Multiscale simulation-based structural predictions of metalloproteins of pharmacological relevance

Paolo Carloni, 2017 .

Structural properties of polyglutamine aggregates investigated via molecular dynamics simulations.

Alessandra Magistrato, Paolo Carloni, Annalisa Pastore, 2008, The journal of physical chemistry. B.

Protonation state of Asp120 in the binuclear active site of the metallo-beta-lactamase from Bacteroides fragilis.

Matteo Dal Peraro, Paolo Carloni, Alejandro J Vila, 2003, Inorganic chemistry.

Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility

Paolo Carloni, P. Carloni, B. Sutton, 2008, Proceedings of the National Academy of Sciences.

A structural model of agonist binding to the α3β4 neuronal nicotinic receptor

Paolo Carloni, Andrea Cavalli, Valeria Costa, 2003 .

Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases.

Matteo Dal Peraro, Paolo Carloni, Michael L Klein, 2007, Journal of the American Chemical Society.

Catabolite activator protein in aqueous solution: a molecular simulation study.

Paolo Carloni, Sergio Pantano, Marco Berrera, 2007, The journal of physical chemistry. B.

Nonempirical Calculations of a Hydrated RNA Duplex

Michele Parrinello, Paolo Carloni, Jürg Hutter, 1996 .

Microseconds dynamics simulations of the outer-membrane protease T.

Marilisa Neri, Marc Baaden, Amos Maritan, 2008, Biophysical journal.

Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations.

Francesco Luigi Gervasio, Matteo Dal Peraro, Paolo Carloni, 2007, Current opinion in structural biology.

ELECTRONIC STRUCTURE OF THE CU, ZN SUPEROXIDE DISMUTASE ACTIVE SITE AND ITS INTERACTIONS WITH THE SUBSTRATE

Michele Parrinello, Paolo Carloni, M. Parrinello, 1995 .

Chasing the full free energy landscape of neuroreceptor/ligand unbinding by metadynamics simulations

Michele Parrinello, Paolo Carloni, Riccardo Capelli, 2019, bioRxiv.

SELF-ASSEMBLED PEPTIDE NANOTUBES FROM FIRST PRINCIPLES

Michele Parrinello, Paolo Carloni, Wanda Andreoni, 1997 .

Hybrid Molecular Mechanics/Coarse-Grained Simulations for Structural Prediction of G-Protein Coupled Receptor/Ligand Complexes

Paolo Carloni, Chuong Nguyen, Alejandro Giorgetti, 2012, PloS one.

Structural Determinants for the Binding of Morphinan Agonists to the μ-Opioid Receptor

Markus Wagener, Pablo Campomanes, Achim Kless, 2015, PloS one.

Insight into the Mechanism of Intramolecular Inhibition of the Catalytic Activity of Sirtuin 2 (SIRT2)

Paolo Carloni, Giulia Rossetti, Bernhard Lüscher, 2015, PloS one.

Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations

Ursula Rothlisberger, Paolo Carloni, S. Piana, 2004 .

The Role and Perspective of ab initio Molecular Dynamics in the Study of Biological Systems

Ursula Rothlisberger, Michele Parrinello, Paolo Carloni, 2002 .

DFT modeling of biological systems

Francesco Luigi Gervasio, Paolo Carloni, Simone Raugei, 2006 .

Drug resistance in HIV‐1 protease: Flexibility‐assisted mechanism of compensatory mutations

Ursula Rothlisberger, Paolo Carloni, S. Piana, 2002, Protein science : a publication of the Protein Society.

Coordination numbers of K(+) and Na(+) Ions inside the selectivity filter of the KcsA potassium channel: insights from first principles molecular dynamics.

Ursula Rothlisberger, Paolo Carloni, Leonardo Guidoni, 2010, Biophysical journal.

Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease.

Michele Parrinello, Paolo Carloni, M. Parrinello, 2002, Journal of molecular biology.

Insights into the Binding of Phenyltiocarbamide (PTC) Agonist to Its Target Human TAS2R38 Bitter Receptor

Paolo Gasparini, Paolo Carloni, Alejandro Giorgetti, 2010, PloS one.

Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases.

Ursula Rothlisberger, Michele Cascella, Paolo Carloni, 2005, Journal of the American Chemical Society.

Sliding of alkylating anticancer drugs along the minor groove of DNA: new insights on sequence selectivity.

Alessandra Magistrato, Attilio V Vargiu, Paolo Carloni, 2008, Biophysical journal.

Key Steps of the cis-Platin-DNA Interaction: Density Functional Theory-Based Molecular Dynamics Simulations

Paolo Carloni, Wanda Andreoni, W. Andreoni, 2000 .

The role and perspective of ab initio molecular dynamics in the study of biological systems.

Ursula Rothlisberger, Michele Parrinello, Paolo Carloni, 2002, Accounts of chemical research.

MiMiC: Multiscale Modeling in Computational Chemistry

Ursula Rothlisberger, Emiliano Ippoliti, Paolo Carloni, 2020, Frontiers in Molecular Biosciences.

Binding of novel azole-bridged dinuclear platinum(II) anticancer drugs to DNA: insights from hybrid QM/MM molecular dynamics simulations.

Alessandra Magistrato, Jan Reedijk, Paolo Carloni, 2006, The journal of physical chemistry. B.

A Computational Model for Protein Ionization by Electrospray Based on Gas-Phase Basicity

Paolo Carloni, Roberto Marchese, Rita Grandori, 2012, Journal of The American Society for Mass Spectrometry.

Statistical analysis of σ-holes: a novel complementary view on halogen bonding.

Pavel Hobza, Paolo Carloni, P. Carloni, 2014, Physical chemistry chemical physics : PCCP.

Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 transactivation responsive RNA.

Gabriele Varani, Paolo Carloni, Giulia Rossetti, 2014, Journal of the American Chemical Society.

Common mechanistic features among metallo-beta-lactamases: a computational study of Aeromonas hydrophila CphA enzyme.

Alessandra Magistrato, Matteo Dal Peraro, Paolo Carloni, 2009, The Journal of biological chemistry.

Molecular view of ligands specificity for CAG repeats in anti-Huntington therapy.

Paolo Carloni, Giulia Rossetti, Oriana Tabarrini, 2015, Journal of chemical theory and computation.

Electronic structure of wet DNA.

Francesco Luigi Gervasio, Michele Parrinello, Paolo Carloni, 2002, Physical review letters.

Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases.

Ursula Rothlisberger, Michele Cascella, Paolo Carloni, 2005 .

Polarization effects and charge transfer in the KcsA potassium channel.

Ursula Rothlisberger, Matteo Dal Peraro, Paolo Carloni, 2006, Biophysical chemistry.

Dynamics and energetics of water permeation through the aquaporin channel

Michele Cascella, Paolo Carloni, Pietro Vidossich, 2004, Proteins.

Evidence for a Transient Additional Ligand Binding Site in the TAS2R46 Bitter Taste Receptor.

Paolo Carloni, Alejandro Giorgetti, Francesco Musiani, 2015, Journal of chemical theory and computation.

Conformational flexibility of the catalytic Asp dyad in HIV‐1 protease: An ab initio study on the free enzyme

Paolo Carloni, S. Piana, P. Carloni, 2000, Proteins.

Docking Ligands on Protein Surfaces: The Case Study of Prion Protein.

Maria Laura Bolognesi, Paolo Carloni, Andrea Cavalli, 2009, Journal of chemical theory and computation.

GOMoDo: A GPCRs Online Modeling and Docking Webserver

Paolo Carloni, Alejandro Giorgetti, Francesco Musiani, 2013, PloS one.

Role of phosphorylated Thr160 for the activation of the CDK2/Cyclin A complex

Maurizio Recanatini, Paolo Carloni, Giovanni Bottegoni, 2005, Proteins.

Quantum medicinal chemistry

Frank Alber, Paolo Carloni, P. Carloni, 2003 .

Solute-solvent charge transfer in aqueous solution.

Matteo Dal Peraro, Paolo Carloni, Simone Raugei, 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

Advanced Computational Methods in Molecular Medicine

Paolo Carloni, Alejandro Giorgetti, Paolo Ruggerone, 2012, Journal of biomedicine & biotechnology.

Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for lateral proton diffusion

Chao Zhang, Trung Hai Nguyen, Peter Pohl, 2012, Proceedings of the National Academy of Sciences.

Molecular basis of the allosteric mechanism of cAMP in the regulatory PKA subunit

Paolo Carloni, Sergio Pantano, Manuela Zaccolo, 2005, FEBS letters.

Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile.

Cecilia Clementi, Wenwei Zheng, Paolo Carloni, 2013, The Journal of chemical physics.

Coarse-grained model of proteins incorporating atomistic detail of the active site.

Marilisa Neri, Amos Maritan, Michele Cascella, 2005, Physical review letters.

Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods

Alessandra Magistrato, Michal Otyepka, Jiří Damborský, 2008, Proteins.

Calculation of redox properties: understanding short- and long-range effects in rubredoxin.

Joost VandeVondele, Michiel Sprik, Paolo Carloni, 2007, The journal of physical chemistry. B.

Dissociation of minor groove binders from DNA: insights from metadynamics simulations

Alessandra Magistrato, Paolo Carloni, Paolo Ruggerone, 2008, Nucleic acids research.

Maurizio Recanatini, Paolo Carloni, Andrea Cavalli, 2006, Chemical reviews.