Performance Characterization of a Molecular Dynamics Code on PC Clusters: Is There Any Easy Parallelism in CHARMM?. - Michela Taufer; Egon Perathoner; Andrea Cavalli; Amedeo Caflisch; Thomas Stricker (IPDPS, 2002)

Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform. - Bennet Uk; Michela Taufer; Thomas Stricker; Giovanni Settanni; Andrea Cavalli; Amedeo Caflisch (CCGRID, 2003)

Implementation and Characterization of Protein Folding on a Desktop Computational Grid - Is CHARMM a Suitable Candidate for the United Devices MetaProcessor? - Bennet Uk; Michela Taufer; Thomas Stricker; Giovanni Settanni; Andrea Cavalli (IPDPS, 2003)

AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets. - Giovanni Bottegoni; Walter Rocchia; Maurizio Recanatini; Andrea Cavalli (ISMB (Supplement of Bioinformatics), 2006)

A Comparative Study on the Application of Hierarchical-Agglomerative Clustering Approaches to Organize Outputs of Reiterated Docking Runs. - Giovanni Bottegoni; Andrea Cavalli; Maurizio Recanatini (J. Chem. Inf. Model., 2006)

Alpha7 nicotinic acetylcholine receptor agonists: Prediction of their binding affinity through a molecular mechanics Poisson-Boltzmann surface area approach. - Giovanni Grazioso; Andrea Cavalli; Marco De Amici; Maurizio Recanatini; Carlo De Micheli (J. Comput. Chem., 2008)

Modeling the hERG potassium channel in a phospholipid bilayer: Molecular dynamics and drug docking studies. - Matteo Masetti; Andrea Cavalli; Maurizio Recanatini (J. Comput. Chem., 2008)

Mechanical Features of Plasmodium falciparum Acyl Carrier Protein in the Delivery of Substrates. - Francesco Colizzi; Maurizio Recanatini; Andrea Cavalli (J. Chem. Inf. Model., 2008)

Insights into docking and scoring neuronal alpha4beta2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations. - Jacopo Sgrignani; Claudia Bonaccini; Giovanni Grazioso; Matteo Chioccioli; Andrea Cavalli; Paola Gratteri (J. Comput. Chem., 2009)

An Innovative Protocol for Comparing Protein Binding Sites via Atomic Grid Maps. - Manuele Bicego; Angelo D. Favia; Paola Bisignano; Andrea Cavalli; Vittorio Murino (KDIR, 2011)

SERAPhiC: A Benchmark for in Silico Fragment-Based Drug Design. - Angelo D. Favia; Giovanni Bottegoni; Irene Nobeli; Paola Bisignano; Andrea Cavalli (J. Chem. Inf. Model., 2011)

In Silico Deconstruction of ATP-Competitive Inhibitors of Glycogen Synthase Kinase-3β. - Paola Bisignano; Chiara Lambruschini; Manuele Bicego; Vittorio Murino; Angelo D. Favia; Andrea Cavalli (J. Chem. Inf. Model., 2012)

Combining Dyad Protonation and Active Site Plasticity in BACE-1 Structure-Based Drug Design. - Puneet Kacker; Matteo Masetti; Martina Mangold; Giovanni Bottegoni; Andrea Cavalli (J. Chem. Inf. Model., 2012)

Collecting and Assessing Human Lactate Dehydrogenase-A Conformations for Structure-Based Virtual Screening. - Rosa Buonfiglio; Mariarosaria Ferraro; Federico Falchi; Andrea Cavalli; Matteo Masetti; Maurizio Recanatini (J. Chem. Inf. Model., 2013)

An Automated Docking Protocol for hERG Channel Blockers. - Giovanni Paolo Di Martino; Matteo Masetti; Luisa Ceccarini; Andrea Cavalli; Maurizio Recanatini (J. Chem. Inf. Model., 2013)

Ionic Dialysance and Conductivity Modeling. - Francesco Locatelli; Celestina Manzoni; Giuseppe Pontoriero; Andrea Cavalli; Salvatore Di Filippo; Ahmad Taher Azar (Modelling and Control of Dialysis Systems (2), 2013)

ALMOST: An all atom molecular simulation toolkit for protein structure determination. - Biao Fu; Aleksandr B. Sahakyan; Carlo Camilloni; Gian Gaetano Tartaglia; Emanuele Paci; Amedeo Caflisch; Michele Vendruscolo; Andrea Cavalli (J. Comput. Chem., 2014)

Kinetic Characterization of Fragment Binding in AmpC β-Lactamase by High-Throughput Molecular Simulations. - Paola Bisignano; Stefan Doerr; Matt J. Harvey; Angelo D. Favia; Andrea Cavalli; Gianni De Fabritiis (J. Chem. Inf. Model., 2014)

Steered Molecular Dynamics Simulations for Studying Protein-Ligand Interaction in Cyclin-Dependent Kinase 5. - Jagdish Suresh Patel; Anna Berteotti; Simone Ronsisvalle; Walter Rocchia; Andrea Cavalli (J. Chem. Inf. Model., 2014)

Allosteric Modulation of Alpha7 Nicotinic Receptors: Mechanistic Insight through Metadynamics and Essential Dynamics. - Giovanni Grazioso; Jacopo Sgrignani; Romina Capelli; Carlo Matera; Clelia Dallanoce; Marco De Amici; Andrea Cavalli (J. Chem. Inf. Model., 2015)

Structure-Based Predictions of Activity Cliffs. - Jarmila Husby; Giovanni Bottegoni; Irina Kufareva; Ruben Abagyan; Andrea Cavalli (J. Chem. Inf. Model., 2015)

Unveiling the Atomic-Level Determinants of Acylase-Ligand Complexes: An Experimental and Computational Study. - Luca Mollica; Gianluca Conti; Loredano Pollegioni; Andrea Cavalli; Elena Rosini (J. Chem. Inf. Model., 2015)

A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins. - Francesca Spyrakis; Paolo Benedetti; Sergio Decherchi; Walter Rocchia; Andrea Cavalli; Stefano Alcaro; Francesco Ortuso; Massimo Baroni; Gabriele Cruciani (J. Chem. Inf. Model., 2015)

Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets. - Giulia Palermo; Inga Bauer; Pablo Campomanes; Andrea Cavalli; Andrea Armirotti; Stefania Girotto; Ursula Rothlisberger; Marco de Vivo (PLoS Comput. Biol., 2015)

Development of a multisite model for Ni(II) ion in solution from thermodynamic and kinetic data. - Matteo Masetti; Francesco Musiani; Mattia Bernetti; Federico Falchi; Andrea Cavalli; Stefano Ciurli; Maurizio Recanatini (J. Comput. Chem., 2017)

Simple Learning with a Teacher via Biased Regularized Least Squares. - Sergio Decherchi; Andrea Cavalli (LOD, 2018)

Binding Residence Time through Scaled Molecular Dynamics: A Prospective Application to hDAAO Inhibitors. - Mattia Bernetti; Elena Rosini; Luca Mollica; Matteo Masetti; Loredano Pollegioni; Maurizio Recanatini; Andrea Cavalli (J. Chem. Inf. Model., 2018)

Fully Flexible Docking via Reaction-Coordinate-Independent Molecular Dynamics Simulations. - Martina Bertazzo; Mattia Bernetti; Maurizio Recanatini; Matteo Masetti; Andrea Cavalli (J. Chem. Inf. Model., 2018)

BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery. - Sergio Decherchi; Giovanni Bottegoni; Andrea Spitaleri; Walter Rocchia; Andrea Cavalli (J. Chem. Inf. Model., 2018)

Addendum to BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery. - Sergio Decherchi; Giovanni Bottegoni; Andrea Spitaleri; Walter Rocchia; Andrea Cavalli (J. Chem. Inf. Model., 2018)

Predicting Residence Time and Drug Unbinding Pathway through Scaled Molecular Dynamics. - Doris A. Schuetz; Mattia Bernetti; Martina Bertazzo; Djordje Musil; Hans-Michael Eggenweiler; Maurizio Recanatini; Matteo Masetti; Gerhard F. Ecker; Andrea Cavalli (J. Chem. Inf. Model., 2019)

Spathial: an R package for the evolutionary analysis of biological data. - Erika Gardini; Federico M. Giorgi; Sergio Decherchi; Andrea Cavalli (Bioinform., 2020)

Exploring Conformational Dynamics of the Extracellular Venus flytrap Domain of the GABAB Receptor: A Path-Metadynamics Study. - Linn S. M. Evenseth; Riccardo Ocello; Mari Gabrielsen; Matteo Masetti; Maurizio Recanatini; Ingebrigt Sylte; Andrea Cavalli (J. Chem. Inf. Model., 2020)

Fast and Memory-Efficient Import Vector Domain Description. - Sergio Decherchi; Andrea Cavalli (Neural Process. Lett., 2020)

An Ab Initio Local Principal Path Algorithm. - Erika Gardini; Andrea Cavalli; Sergio Decherchi (IJCNN, 2021)

On the Stability of Feature Selection in Multiomics Data. - Luca Pestarino; Giovanni Fiorito; Silvia Polidoro; Paolo Vineis; Andrea Cavalli; Sergio Decherchi (IJCNN, 2021)

Using Principal Paths to Walk Through Music and Visual Art Style Spaces Induced by Convolutional Neural Networks. - Erika Gardini; Marco Jacopo Ferrarotti; Andrea Cavalli; Sergio Decherchi (Cogn. Comput., 2021)

Targeting the JAK/STAT Pathway: A Combined Ligand- and Target-Based Approach. - 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 (J. Chem. Inf. Model., 2021)

Assessing the Effectiveness of Non-Turing Computing Paradigms. - Lorenzo Rocutto; Marco Maronese; Fabio Lorenzo Traversa; Sergio Decherchi; Andrea Cavalli (IEEE Access, 2023)

Molecular Dynamics and Machine Learning Give Insights on the Flexibility-Activity Relationships in Tyrosine Kinome. - Sarmistha Majumdar; Francesco Di Palma; Francesca Spyrakis; Sergio Decherchi; Andrea Cavalli (J. Chem. Inf. Model., 2023)

Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation? - Pedro R. A. S. Bassi; Wenxuan Li; Yucheng Tang; Fabian Isensee; Zifu Wang; Jieneng Chen; Yu-Cheng Chou; Yannick Kirchhoff; Maximilian Rokuss; Ziyan Huang; Jin Ye 002; Junjun He; et al. (NeurIPS, 2024)

Faster ISNet for Background Bias Mitigation on Deep Neural Networks. - Pedro R. A. S. Bassi; Sergio Decherchi; Andrea Cavalli (IEEE Access, 2024)

Explanation is All You Need in Distillation: Mitigating Bias and Shortcut Learning. - Pedro R. A. S. Bassi; Andrea Cavalli; Sergio Decherchi (CoRR, 2024)

Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation? - Pedro R. A. S. Bassi; Wenxuan Li; Yucheng Tang; Fabian Isensee; Zifu Wang; Jieneng Chen; Yu-Cheng Chou; Yannick Kirchhoff; Maximilian Rokuss; Ziyan Huang; Jin Ye 002; Junjun He; et al. (CoRR, 2024)

Comparing Adiabatic Quantum Computers for satellite images feature extraction. - Lorenzo Rocutto; Marco Maronese; Daniele Dragoni; Andrea Cavalli; Carlo Cavazzoni (Future Gener. Comput. Syst., 2024)

AMCG: a graph dual atomic-molecular conditional molecular generator. - Carlo Abate; Sergio Decherchi; Andrea Cavalli (Mach. Learn. Sci. Technol., 2024)

AI-Driven CAD for Histological Analysis in Mountain Regions: Advancing Local Healthcare and Sustainable Development. - Matteo Calabrese; Chiara B. Salvemini; Michela Assale; Stefano Sartor; Roberta Patetta; Laura Caramanico; Andrea Cavalli; Stefano Gustincich; Jean Marc Christille (BDAI, 2025)

Label Critic: Design Data Before Models. - Pedro R. A. S. Bassi; Qilong Wu; Wenxuan Li; Sergio Decherchi; Andrea Cavalli; Alan L. Yuille; Zongwei Zhou (ISBI, 2025)

Learning Segmentation from Radiology Reports. - Pedro R. A. S. Bassi; Wenxuan Li; Jieneng Chen; Zheren Zhu; Tianyu Lin; Sergio Decherchi; Andrea Cavalli; Kang Wang 016; Yang Yang 009; Alan L. Yuille; Zongwei Zhou (MICCAI (5), 2025)

NanoShaperWeb: Molecular Surface and Pocket Detection Made Visual. - Carlo Abate; Eleonora Serra; Walter Rocchia; Andrea Cavalli; Sergio Decherchi (J. Chem. Inf. Model., 2025)

Path-Based Nonequilibrium Binding Free Energy Estimation, from Protein-Ligand to RNA-Ligand Binding. - Eleonora Serra; Alessia Ghidini; Riccardo Aguti; Mattia Bernetti; Sergio Decherchi; Andrea Cavalli (J. Chem. Inf. Model., 2025)

RadGPT: Constructing 3D Image-Text Tumor Datasets. - Pedro R. A. S. Bassi; Mehmet Can Yavuz; Kang Wang 016; Xiaoxi Chen; Wenxuan Li; Sergio Decherchi; Andrea Cavalli; Yang Yang 009; Alan L. Yuille; Zongwei Zhou (CoRR, 2025)

Scaling Artificial Intelligence for Multi-Tumor Early Detection with More Reports, Fewer Masks. - Pedro R. A. S. Bassi; Xinze Zhou; Wenxuan Li; Szymon Plotka; Jieneng Chen; Qi Chen 014; Zheren Zhu; Jakub Przado; Ibrahim E. Hamaci; Sezgin Er; Yuhan Wang 001; Ashwin Kumar; et al. (CoRR, 2025)