Andrea Cavalli

Publication Activity (10 Years)

Years Active: 2002-2024
Publications (10 Years): 19

Top Topics

Biological Data

Molecular Dynamics

Protein Structure

Top Venues

J. Chem. Inf. Model.

J. Comput. Chem.

Publications

Pedro R. A. S. Bassi, Andrea Cavalli, Sergio Decherchi
Explanation is All You Need in Distillation: Mitigating Bias and Shortcut Learning. CoRR (2024)
Pedro R. A. S. Bassi, Sergio Decherchi, Andrea Cavalli
Faster ISNet for Background Bias Mitigation on Deep Neural Networks. CoRR (2024)
Lorenzo Rocutto, Marco Maronese, Daniele Dragoni, Andrea Cavalli, Carlo Cavazzoni
Comparing Adiabatic Quantum Computers for satellite images feature extraction. Future Gener. Comput. Syst. 159 (2024)
Lorenzo Rocutto, Marco Maronese, Fabio Lorenzo Traversa, Sergio Decherchi, Andrea Cavalli
Assessing the Effectiveness of Non-Turing Computing Paradigms. IEEE Access 11 (2023)
Sarmistha Majumdar, Francesco Di Palma, Francesca Spyrakis, Sergio Decherchi, Andrea Cavalli
Molecular Dynamics and Machine Learning Give Insights on the Flexibility-Activity Relationships in Tyrosine Kinome. J. Chem. Inf. Model. 63 (15) (2023)
Erika Gardini, Andrea Cavalli, Sergio Decherchi
An Ab Initio Local Principal Path Algorithm. IJCNN (2021)
Erika Gardini, Marco Jacopo Ferrarotti, Andrea Cavalli, Sergio Decherchi
Using Principal Paths to Walk Through Music and Visual Art Style Spaces Induced by Convolutional Neural Networks. Cogn. Comput. 13 (2) (2021)
Luca Pestarino, Giovanni Fiorito, Silvia Polidoro, Paolo Vineis, Andrea Cavalli, Sergio Decherchi
On the Stability of Feature Selection in Multiomics Data. IJCNN (2021)
María Gálvez-Llompart, Riccardo Ocello, Laura Rullo, Serena Stamatakos, Irene Alessandrini, Riccardo Zanni, Iñaki Tuñón, Andrea Cavalli, Sanzio Candeletti, Matteo Masetti, Patrizia Romualdi, Maurizio Recanatini
Targeting the JAK/STAT Pathway: A Combined Ligand- and Target-Based Approach. J. Chem. Inf. Model. 61 (6) (2021)
Sergio Decherchi, Andrea Cavalli
Fast and Memory-Efficient Import Vector Domain Description. Neural Process. Lett. 52 (1) (2020)
Erika Gardini, Federico M. Giorgi, Sergio Decherchi, Andrea Cavalli
Spathial: an R package for the evolutionary analysis of biological data. Bioinform. 36 (17) (2020)
Linn S. M. Evenseth, Riccardo Ocello, Mari Gabrielsen, Matteo Masetti, Maurizio Recanatini, Ingebrigt Sylte, Andrea Cavalli
Exploring Conformational Dynamics of the Extracellular Venus flytrap Domain of the GABAB Receptor: A Path-Metadynamics Study. J. Chem. Inf. Model. 60 (4) (2020)
Doris A. Schuetz, Mattia Bernetti, Martina Bertazzo, Djordje Musil, Hans-Michael Eggenweiler, Maurizio Recanatini, Matteo Masetti, Gerhard F. Ecker, Andrea Cavalli
Predicting Residence Time and Drug Unbinding Pathway through Scaled Molecular Dynamics. J. Chem. Inf. Model. 59 (1) (2019)
Sergio Decherchi, Giovanni Bottegoni, Andrea Spitaleri, Walter Rocchia, Andrea Cavalli
Addendum to BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery. J. Chem. Inf. Model. 58 (8) (2018)
Sergio Decherchi, Andrea Cavalli
Simple Learning with a Teacher via Biased Regularized Least Squares. LOD (2018)
Sergio Decherchi, Giovanni Bottegoni, Andrea Spitaleri, Walter Rocchia, Andrea Cavalli
BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery. J. Chem. Inf. Model. 58 (2) (2018)
Martina Bertazzo, Mattia Bernetti, Maurizio Recanatini, Matteo Masetti, Andrea Cavalli
Fully Flexible Docking via Reaction-Coordinate-Independent Molecular Dynamics Simulations. J. Chem. Inf. Model. 58 (2) (2018)
Mattia Bernetti, Elena Rosini, Luca Mollica, Matteo Masetti, Loredano Pollegioni, Maurizio Recanatini, Andrea Cavalli
Binding Residence Time through Scaled Molecular Dynamics: A Prospective Application to hDAAO Inhibitors. J. Chem. Inf. Model. 58 (11) (2018)
Matteo Masetti, Francesco Musiani, Mattia Bernetti, Federico Falchi, Andrea Cavalli, Stefano Ciurli, Maurizio Recanatini
Development of a multisite model for Ni(II) ion in solution from thermodynamic and kinetic data. J. Comput. Chem. 38 (21) (2017)
Francesca Spyrakis, Paolo Benedetti, Sergio Decherchi, Walter Rocchia, Andrea Cavalli, Stefano Alcaro, Francesco Ortuso, Massimo Baroni, Gabriele Cruciani
A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins. J. Chem. Inf. Model. 55 (10) (2015)
Giovanni Grazioso, Jacopo Sgrignani, Romina Capelli, Carlo Matera, Clelia Dallanoce, Marco De Amici, Andrea Cavalli
Allosteric Modulation of Alpha7 Nicotinic Receptors: Mechanistic Insight through Metadynamics and Essential Dynamics. J. Chem. Inf. Model. 55 (12) (2015)
Giulia Palermo, Inga Bauer, Pablo Campomanes, Andrea Cavalli, Andrea Armirotti, Stefania Girotto, Ursula Rothlisberger, Marco de Vivo
Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets. PLoS Comput. Biol. 11 (6) (2015)
Jarmila Husby, Giovanni Bottegoni, Irina Kufareva, Ruben Abagyan, Andrea Cavalli
Structure-Based Predictions of Activity Cliffs. J. Chem. Inf. Model. 55 (5) (2015)
Luca Mollica, Gianluca Conti, Loredano Pollegioni, Andrea Cavalli, Elena Rosini
Unveiling the Atomic-Level Determinants of Acylase-Ligand Complexes: An Experimental and Computational Study. J. Chem. Inf. Model. 55 (10) (2015)
Jagdish Suresh Patel, Anna Berteotti, Simone Ronsisvalle, Walter Rocchia, Andrea Cavalli
Steered Molecular Dynamics Simulations for Studying Protein-Ligand Interaction in Cyclin-Dependent Kinase 5. J. Chem. Inf. Model. 54 (2) (2014)
Paola Bisignano, Stefan Doerr, Matt J. Harvey, Angelo D. Favia, Andrea Cavalli, Gianni De Fabritiis
Kinetic Characterization of Fragment Binding in AmpC β-Lactamase by High-Throughput Molecular Simulations. J. Chem. Inf. Model. 54 (2) (2014)
Biao Fu, Aleksandr B. Sahakyan, Carlo Camilloni, Gian Gaetano Tartaglia, Emanuele Paci, Amedeo Caflisch, Michele Vendruscolo, Andrea Cavalli
ALMOST: An all atom molecular simulation toolkit for protein structure determination. J. Comput. Chem. 35 (14) (2014)
Giovanni Paolo Di Martino, Matteo Masetti, Luisa Ceccarini, Andrea Cavalli, Maurizio Recanatini
An Automated Docking Protocol for hERG Channel Blockers. J. Chem. Inf. Model. 53 (1) (2013)
Rosa Buonfiglio, Mariarosaria Ferraro, Federico Falchi, Andrea Cavalli, Matteo Masetti, Maurizio Recanatini
Collecting and Assessing Human Lactate Dehydrogenase-A Conformations for Structure-Based Virtual Screening. J. Chem. Inf. Model. 53 (11) (2013)
Puneet Kacker, Matteo Masetti, Martina Mangold, Giovanni Bottegoni, Andrea Cavalli
Combining Dyad Protonation and Active Site Plasticity in BACE-1 Structure-Based Drug Design. J. Chem. Inf. Model. 52 (5) (2012)
Paola Bisignano, Chiara Lambruschini, Manuele Bicego, Vittorio Murino, Angelo D. Favia, Andrea Cavalli
In Silico Deconstruction of ATP-Competitive Inhibitors of Glycogen Synthase Kinase-3β. J. Chem. Inf. Model. 52 (12) (2012)
Angelo D. Favia, Giovanni Bottegoni, Irene Nobeli, Paola Bisignano, Andrea Cavalli
SERAPhiC: A Benchmark for in Silico Fragment-Based Drug Design. J. Chem. Inf. Model. 51 (11) (2011)
Manuele Bicego, Angelo D. Favia, Paola Bisignano, Andrea Cavalli, Vittorio Murino
An Innovative Protocol for Comparing Protein Binding Sites via Atomic Grid Maps. KDIR (2011)
Jacopo Sgrignani, Claudia Bonaccini, Giovanni Grazioso, Matteo Chioccioli, Andrea Cavalli, Paola Gratteri
Insights into docking and scoring neuronal alpha4beta2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations. J. Comput. Chem. 30 (15) (2009)
Giovanni Grazioso, Andrea Cavalli, Marco De Amici, Maurizio Recanatini, Carlo De Micheli
Alpha7 nicotinic acetylcholine receptor agonists: Prediction of their binding affinity through a molecular mechanics Poisson-Boltzmann surface area approach. J. Comput. Chem. 29 (15) (2008)
Francesco Colizzi, Maurizio Recanatini, Andrea Cavalli
Acyl Carrier Protein in the Delivery of Substrates. J. Chem. Inf. Model. 48 (12) (2008)
Matteo Masetti, Andrea Cavalli, Maurizio Recanatini
Modeling the hERG potassium channel in a phospholipid bilayer: Molecular dynamics and drug docking studies. J. Comput. Chem. 29 (5) (2008)
Giovanni Bottegoni, Andrea Cavalli, Maurizio Recanatini
A Comparative Study on the Application of Hierarchical-Agglomerative Clustering Approaches to Organize Outputs of Reiterated Docking Runs. J. Chem. Inf. Model. 46 (2) (2006)
Giovanni Bottegoni, Walter Rocchia, Maurizio Recanatini, Andrea Cavalli
AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets. ISMB (Supplement of Bioinformatics) (2006)
Bennet Uk, Michela Taufer, Thomas Stricker, Giovanni Settanni, Andrea Cavalli, Amedeo Caflisch
Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform. CCGRID (2003)
Bennet Uk, Michela Taufer, Thomas Stricker, Giovanni Settanni, Andrea Cavalli
Implementation and Characterization of Protein Folding on a Desktop Computational Grid - Is CHARMM a Suitable Candidate for the United Devices MetaProcessor? IPDPS (2003)
Michela Taufer, Egon Perathoner, Andrea Cavalli, Amedeo Caflisch, Thomas Stricker
Performance Characterization of a Molecular Dynamics Code on PC Clusters: Is There Any Easy Parallelism in CHARMM?. IPDPS (2002)