Paolo Carloni

27 papers Journal 27
YearRankTypeTitle / Venue / Authors
2026 J jnl
MiMiCPy-FM: A User-Friendly Force Matching Tool for Extending the Time Scale of QM/MM MD MiMiC Simulations.
J. Chem. Inf. Model.
Sachin Shivakumar, Giorgia Frumenzio, Francesco Musiani, Fabio Affinito, Emiliano Ippoliti, Bharath Raghavan, Giulia Rossetti, Davide Mandelli, Paolo Carloni
2025 J jnl
Common characteristics of variants linked to autism spectrum disorder in the WAVE regulatory complex.
Frontiers Comput. Neurosci.
Song Xie, Ke Zuo, Silvia De Rubeis, Giorgio Bonollo, Giorgio Colombo, Paolo Ruggerone, Paolo Carloni
2025 J jnl
Impact of Genetic Variants Associated with Neurodevelopmental Disorders on the WAVE Regulatory Complex.
J. Chem. Inf. Model.
Song Xie, Ke Zuo, Silvia De Rubeis, Giorgio Bonollo, Giorgio Colombo, Paolo Ruggerone, Paolo Carloni
2025 J jnl
Role of Residues Undergoing Hereditary Spastic Paraplegias Mutations: Insights from Simulating the Spiral to Ring Transition in Katanin.
J. Chem. Inf. Model.
Maria S. Kelly, Riccardo Capelli, Ruxandra I. Dima, Paolo Carloni
2024 J jnl
3D DFT by block tensor-matrix multiplication via a modified Cannon's algorithm: Implementation and scaling on distributed-memory clusters with fat tree networks.
J. Parallel Distributed Comput.
Nitin Malapally, Viacheslav Bolnykh, Estela Suarez, Paolo Carloni, Thomas Lippert, Davide Mandelli
2024 J jnl
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution.
J. Chem. Inf. Model.
Emile de Bruyn, Anton Emil Dorn, Giulia Rossetti, Claudio Fernandez, Tiago F. Outeiro, Jörg B. Schulz, Paolo Carloni
2024 J jnl
Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease.
J. Chem. Inf. Model.
Simone Albani, Elisa Costanzi, Gia Linh Hoang, Maria Kuzikov, Marcus Frings, Narjes Ansari, Nicola Demitri, Toan T. Nguyen, Valerio Rizzi, Jörg B. Schulz, Carsten Bolm, Andrea Zaliani, Paolo Carloni, Paola Storici, Giulia Rossetti
2023 J jnl
Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations.
J. Chem. Inf. Model.
Bharath Raghavan, Mirko Paulikat, Katya Ahmad, Lara Callea, Andrea Rizzi, Emiliano Ippoliti, Davide Mandelli, Laura Bonati, Marco de Vivo, Paolo Carloni
2023 J jnl
Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel.
J. Chem. Inf. Model.
Florian Karl Schackert, Johann Biedermann, Saeid Abdolvand, Sonja Minniberger, Chen Song, Andrew J. R. Plested, Paolo Carloni, Han Sun
2023 J jnl
MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations.
J. Chem. Inf. Model.
Bharath Raghavan, Florian K. Schackert, Andrea Levy, Sophia K. Johnson, Emiliano Ippoliti, Davide Mandelli, Jógvan Magnus Haugaard Olsen, Ursula Rothlisberger, Paolo Carloni
2023 J jnl
Molecular Dynamics and Structural Studies of Zinc Chloroquine Complexes.
J. Chem. Inf. Model.
Mirko Paulikat, Daniele Vitone, Florian Karl Schackert, Nils Schuth, Alessandra Barbanente, GiovanniMaria Piccini, Emiliano Ippoliti, Giulia Rossetti, Adam H. Clark, Maarten Nachtegaal, Michael Haumann, Holger Dau, Paolo Carloni, Silvano Geremia, Rita De Zorzi, Liliana Quintanar, Fabio Arnesano
2023 J jnl
Physical Chemistry of Chloroquine Permeation through the Cell Membrane with Atomistic Detail.
J. Chem. Inf. Model.
Mirko Paulikat, GiovanniMaria Piccini, Emiliano Ippoliti, Giulia Rossetti, Fabio Arnesano, Paolo Carloni
2023 J jnl
Predictions of the Poses and Affinity of a Ligand over the Entire Surface of a NEET Protein: The Case of Human MitoNEET.
J. Chem. Inf. Model.
Ke Zuo, Riccardo Capelli, Giulia Rossetti, Rachel Nechushtai, Paolo Carloni
2023 J jnl
Scalability of 3D-DFT by block tensor-matrix multiplication on the JUWELS Cluster.
CoRR
Nitin Malapally, Viacheslav Bolnykh, Estela Suarez, Paolo Carloni, Thomas Lippert, Davide Mandelli
2020 J jnl
Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-Based Hybrid Molecular Mechanics/Coarse-Grained Approach.
J. Chem. Inf. Model.
Jakob Schneider, Ksenia Korshunova, Zeineb Si Chaib, Alejandro Giorgetti, Mercedes Alfonso-Prieto, Paolo Carloni
2019 J jnl
Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals.
PLoS Comput. Biol.
Neil J. Bruce, Daniele Narzi, Daniel Trpevski, Siri Camee van Keulen, Anu G. Nair, Ursula Rothlisberger, Rebecca C. Wade, Paolo Carloni, Jeanette Hellgren Kotaleski
2018 J jnl
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.
PLoS Comput. Biol.
Anna Bochicchio, Miroslav Krepl, Fan Yang, Gabriele Varani, Jirí Sponer, Paolo Carloni
2017 J jnl
Structural prediction of the interaction of the tumor suppressor p27KIP1 with cyclin A/CDK2 identifies a novel catalytically relevant determinant.
BMC Bioinform.
Jinyu Li, Jörg Vervoorts, Paolo Carloni, Giulia Rossetti, Bernhard Lüscher
2017 J jnl
Unifying view of mechanical and functional hotspots across class A GPCRs.
PLoS Comput. Biol.
Luca Ponzoni, Giulia Rossetti, Luca Maggi, Alejandro Giorgetti, Paolo Carloni, Cristian Micheletti
2014 J jnl
Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer.
PLoS Comput. Biol.
Jinyu Li, Giulia Rossetti, Jens Dreyer, Simone Raugei, Emiliano Ippoliti, Bernhard Lüscher, Paolo Carloni
2012 J jnl
On the active site of mononuclear B1 metallo β-lactamases: a computational study.
J. Comput. Aided Mol. Des.
Jacopo Sgrignani, Alessandra Magistrato, Matteo Dal Peraro, Alejandro J. Vila, Paolo Carloni, Roberta Pierattelli
2011 J jnl
Molecular motions in drug design: the coming age of the metadynamics method.
J. Comput. Aided Mol. Des.
Xevi Biarnés, Salvatore Bongarzone, Attilio Vittorio Vargiu, Paolo Carloni, Paolo Ruggerone
2010 J jnl
On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions.
PLoS Comput. Biol.
Roberto Marchese, Rita Grandori, Paolo Carloni, Simone Raugei
2009 J jnl
Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations.
PLoS Comput. Biol.
Vanessa Leone, Gianluca Lattanzi, Carla Molteni, Paolo Carloni
2008 J jnl
On the nature of the reaction intermediate in the HIV-1 protease: a quantum chemical study.
Comput. Phys. Commun.
V. Carnevale, Simone Raugei, Simone Piana, Paolo Carloni
2008 J jnl
Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure.
J. Comput. Chem.
Katrin Spiegel, Alessandra Magistrato, Patrick Maurer, Paolo Ruggerone, Ursula Rothlisberger, Paolo Carloni, Jan Reedijk, Michael L. Klein
2007 J jnl
Structural models of human big conductance calcium- and voltage-gated potassium channels.
Comput. Phys. Commun.
Agata Kranjc, Claudio Anselmi, Paolo Carloni, Frank E. Blaney