Discovering HDAC class II selective inhibitors by multidisciplinary approach. - Simone Lorenzi; Andrea Beccari; D. Carettoni; M. Rubino; Vanessa Nardese (J. Cheminformatics, 2011)

Use of Experimental Design To Optimize Docking Performance: The Case of LiGenDock, the Docking Module of Ligen, a New De Novo Design Program. - Claudia Beato; Andrea Beccari; Carlo Cavazzoni; Simone Lorenzi; Gabriele Costantino (J. Chem. Inf. Model., 2013)

LiGen: A High Performance Workflow for Chemistry Driven de Novo Design. - Andrea Beccari; Carlo Cavazzoni; Claudia Beato; Gabriele Costantino (J. Chem. Inf. Model., 2013)

ANTAREX - AutoTuning and Adaptivity appRoach for Energy Efficient eXascale HPC Systems. - Cristina Silvano; Giovanni Agosta; Andrea Bartolini; Andrea Beccari; Luca Benini; João M. P. Cardoso; Carlo Cavazzoni; Radim Cmar; Jan Martinovic; Gianluca Palermo; Martin Palkovic; Erven Rohou; et al. (CSE, 2015)

The ANTAREX approach to autotuning and adaptivity for energy efficient HPC systems. - Cristina Silvano; Giovanni Agosta; Stefano Cherubin; Davide Gadioli; Gianluca Palermo; Andrea Bartolini; Luca Benini; Jan Martinovic; Martin Palkovic; Katerina Slaninová; João Bispo; João M. P. Cardoso; et al. (Conf. Computing Frontiers, 2016)

Autotuning and adaptivity approach for energy efficient Exascale HPC systems: The ANTAREX approach. - Cristina Silvano; Giovanni Agosta; Andrea Bartolini; Andrea Rosario Beccari; Luca Benini; João Bispo; Radim Cmar; João M. P. Cardoso; Carlo Cavazzoni; Jan Martinovic; Gianluca Palermo; Martin Palkovic; et al. (DATE, 2016)

The ANTAREX tool flow for monitoring and autotuning energy efficient HPC systems. - Cristina Silvano; Giovanni Agosta; Jorge G. Barbosa; Andrea Bartolini; Andrea Rosario Beccari; Luca Benini; João Bispo; João M. P. Cardoso; Carlo Cavazzoni; Stefano Cherubin; Radim Cmar; Davide Gadioli; et al. (SAMOS, 2017)

Autotuning and adaptivity in energy efficient HPC systems: the ANTAREX toolbox. - Cristina Silvano; Gianluca Palermo; Giovanni Agosta; Amir H. Ashouri; Davide Gadioli; Stefano Cherubin; Emanuele Vitali; Luca Benini; Andrea Bartolini; Daniele Cesarini; João M. P. Cardoso; João Bispo; et al. (CF, 2018)

ANTAREX: A DSL-Based Approach to Adaptively Optimizing and Enforcing Extra-Functional Properties in High Performance Computing. - Cristina Silvano; Giovanni Agosta; Andrea Bartolini; Andrea Rosario Beccari; Luca Benini; Loïc Besnard; João Bispo; Radim Cmar; João M. P. Cardoso; Carlo Cavazzoni; Stefano Cherubin; Davide Gadioli; et al. (DSD, 2018)

Accelerating a Geometric Approach to Molecular Docking with OpenACC. - Emanuele Vitali; Davide Gadioli; Gianluca Palermo; Andrea Beccari; Cristina Silvano (PBio@EuroMPI, 2018)

ADPredict: ADP-ribosylation site prediction based on physicochemical and structural descriptors. - Matteo Lo Monte; Candida Manelfi; Marica Gemei; Daniela Corda; Andrea Rosario Beccari (Bioinform., 2018)

An hybrid approach to accelerate a molecular docking application for virtual screening in heterogeneous nodes: POSTER. - Emanuele Vitali; Davide Gadioli; Andrea Beccari; Carlo Cavazzoni; Cristina Silvano; Gianluca Palermo (CF, 2019)

Supporting the Scale-Up of High Performance Application to Pre-Exascale Systems: The ANTAREX Approach. - Cristina Silvano; Giovanni Agosta; Andrea Bartolini; Andrea Rosario Beccari; Luca Benini; Loïc Besnard; João Bispo; Radim Cmar; João M. P. Cardoso; Carlo Cavazzoni; Daniele Cesarini; Stefano Cherubin; et al. (PDP, 2019)

The ANTAREX Domain Specific Language for High Performance Computing. - Cristina Silvano; Giovanni Agosta; Andrea Bartolini; Andrea Rosario Beccari; Luca Benini; Loïc Besnard; João Bispo; Radim Cmar; João M. P. Cardoso; Carlo Cavazzoni; Daniele Cesarini; Stefano Cherubin; et al. (CoRR, 2019)

Exploiting OpenMP & OpenACC to Accelerate a Molecular Docking Mini-App in Heterogeneous HPC Nodes. - Emanuele Vitali; Davide Gadioli; Gianluca Palermo; Andrea Beccari; Carlo Cavazzoni; Cristina Silvano (CoRR, 2019)

The ANTAREX domain specific language for high performance computing. - Cristina Silvano; Giovanni Agosta; Andrea Bartolini; Andrea Rosario Beccari; Luca Benini; Loïc Besnard; João Bispo; Radim Cmar; João M. P. Cardoso; Carlo Cavazzoni; Daniele Cesarini; Stefano Cherubin; et al. (Microprocess. Microsystems, 2019)

Exploiting OpenMP and OpenACC to accelerate a geometric approach to molecular docking in heterogeneous HPC nodes. - Emanuele Vitali; Davide Gadioli; Gianluca Palermo; Andrea Beccari; Carlo Cavazzoni; Cristina Silvano (J. Supercomput., 2019)

EXSCALATE: An extreme-scale in-silico virtual screening platform to evaluate 1 trillion compounds in 60 hours on 81 PFLOPS supercomputers. - Davide Gadioli; Emanuele Vitali; Federico Ficarelli; Chiara Latini; Candida Manelfi; Carmine Talarico; Cristina Silvano; Carlo Cavazzoni; Gianluca Palermo; Andrea Rosario Beccari (CoRR, 2021)

"Molecular Anatomy": a new multi-dimensional hierarchical scaffold analysis tool. - Candida Manelfi; Marica Gemei; Carmine Talarico; Carmen Cerchia; Anna Fava; Filippo Lunghini; Andrea Rosario Beccari (J. Cheminformatics, 2021)

Tunable approximations to control time-to-solution in an HPC molecular docking Mini-App. - Davide Gadioli; Gianluca Palermo; Stefano Cherubin; Emanuele Vitali; Giovanni Agosta; Candida Manelfi; Andrea Rosario Beccari; Carlo Cavazzoni; Nico Sanna; Cristina Silvano (J. Supercomput., 2021)

An extreme-scale virtual screening platform for drug discovery. - Davide Gadioli; Emanuele Vitali; Federico Ficarelli; Chiara Latini; Candida Manelfi; Carmine Talarico; Cristina Silvano; Andrea Rosario Beccari; Gianluca Palermo (CF, 2022)

Towards a Portable Drug Discovery Pipeline with SYCL 2020. - Luigi Crisci; Majid Salimi Beni; Biagio Cosenza; Nicolò Scipione; Davide Gadioli; Emanuele Vitali; Gianluca Palermo; Andrea Beccari (IWOCL, 2022)

GENEOnet: A new machine learning paradigm based on Group Equivariant Non-Expansive Operators. An application to protein pocket detection. - Giovanni Bocchi; Patrizio Frosini; Alessandra Micheletti; Alessandro Pedretti; Carmen Gratteri; Filippo Lunghini; Andrea Rosario Beccari; Carmine Talarico (CoRR, 2022)

GPU-optimized Approaches to Molecular Docking-based Virtual Screening in Drug Discovery: A Comparative Analysis. - Emanuele Vitali; Federico Ficarelli; Mauro Bisson; Davide Gadioli; Massimiliano Fatica; Andrea Rosario Beccari; Gianluca Palermo (CoRR, 2022)

Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach. - Gianluca Palermo; Gianmarco Accordi; Davide Gadioli; Emanuele Vitali; Cristina Silvano; Bruno Guindani; Danilo Ardagna; Andrea Rosario Beccari; Domenico Bonanni; Carmine Talarico; Filippo Lunghini; Jan Martinovic; et al. (CF, 2023)

Domain-Specific Energy Modeling for Drug Discovery and Magnetohydrodynamics Applications. - Lorenzo Carpentieri; Marco D'Antonio; Kaijie Fan; Luigi Crisci; Biagio Cosenza; Federico Ficarelli; Daniele Cesarini; Gianmarco Accordi; Davide Gadioli; Gianluca Palermo; Peter Thoman; Philip Salzmann; et al. (SC Workshops, 2023)

Improving computation efficiency using input and architecture features for a virtual screening application. - Gianmarco Accordi; Emanuele Vitali; Davide Gadioli; Luigi Crisci; Biagio Cosenza; Mauro Bisson; Massimiliano Fatica; Andrea Beccari; Gianluca Palermo (CoRR, 2023)

EXSCALATE: An Extreme-Scale Virtual Screening Platform for Drug Discovery Targeting Polypharmacology to Fight SARS-CoV-2. - Davide Gadioli; Emanuele Vitali; Federico Ficarelli; Chiara Latini; Candida Manelfi; Carmine Talarico; Cristina Silvano; Carlo Cavazzoni; Gianluca Palermo; Andrea Rosario Beccari (IEEE Trans. Emerg. Top. Comput., 2023)

A non-intrusive data-driven reduced order model for parametrized CFD-DEM numerical simulations. - Arash Hajisharifi; Francesco Romano; Michele Girfoglio; Andrea Beccari; Domenico Bonanni; Gianluigi Rozza (J. Comput. Phys., 2023)

ProfhEX: AI-based platform for small molecules liability profiling. - Filippo Lunghini; Anna Fava; Vincenzo Pisapia; Francesco Sacco; Daniela Iaconis; Andrea Rosario Beccari (J. Cheminformatics, 2023)

LIGATE - LIgand Generator and portable drug discovery platform AT Exascale. - Gianluca Palermo; Gianmarco Accordi; Davide Gadioli; Yuedong Zhang; Emanuele Vitali; Bruno Guindani; Danilo Ardagna; Cristina Silvano; Andrea Rosario Beccari; Domenico Bonanni; Carmine Talarico; Filippo Lunghini; et al. (CF (Companion), 2024)

ZSMILES: An Approach for Efficient SMILES Storage for Random Access in Virtual Screening. - Gianmarco Accordi; Davide Gadioli; Giorgio Seguini; Andrea Rosario Beccari; Gianluca Palermo (IPDPS (Workshops), 2024)

Unlocking performance portability on LUMI-G supercomputer: A virtual screening case study. - Gianmarco Accordi; Davide Gadioli; Gianluca Palermo; Luigi Crisci; Lorenzo Carpentieri; Biagio Cosenza; Andrea Rosario Beccari (IWOCL, 2024)

A geometric XAI approach to protein pocket detection. - Giovanni Bocchi; Patrizio Frosini; Alessandra Micheletti; Alessandro Pedretti; Gianluca Palermo; Davide Gadioli; Carmen Gratteri; Filippo Lunghini; Andrea Rosario Beccari; Anna Fava; Carmine Talarico (xAI (Late-breaking Work, Demos, Doctoral Consortium), 2024)

A LSTM-enhanced surrogate model to simulate the dynamics of particle-laden fluid systems. - Arash Hajisharifi; Rahul Halder; Michele Girfoglio; Andrea Beccari; Domenico Bonanni; Gianluigi Rozza (CoRR, 2024)

Molecular Docking via Weighted Subgraph Isomorphism on Quantum Annealers. - Emanuele Triuzzi; Riccardo Mengoni; Domenico Bonanni; Daniele Ottaviani; Andrea Beccari; Gianluca Palermo (CoRR, 2024)

Exploring the future of biopharmaceutical drug discovery: can advanced AI platforms overcome current challenges? - Alberto Bettanti; Andrea Rosario Beccari; Marco Biccarino (Discov. Artif. Intell., 2024)

Enabling performance portability on the LiGen drug discovery pipeline. - Luigi Crisci; Lorenzo Carpentieri; Biagio Cosenza; Gianmarco Accordi; Davide Gadioli; Emanuele Vitali; Gianluca Palermo; Andrea Rosario Beccari (Future Gener. Comput. Syst., 2024)

GPU-optimized approaches to molecular docking-based virtual screening in drug discovery: A comparative analysis. - Emanuele Vitali; Federico Ficarelli; Mauro Bisson; Davide Gadioli; Gianmarco Accordi; Massimiliano Fatica; Andrea Rosario Beccari; Gianluca Palermo (J. Parallel Distributed Comput., 2024)

Out of kernel tuning and optimizations for portable large-scale docking experiments on GPUs. - Gianmarco Accordi; Davide Gadioli; Emanuele Vitali; Luigi Crisci; Biagio Cosenza; Andrea Beccari; Gianluca Palermo (J. Supercomput., 2024)

"DompeKeys": a set of novel substructure-based descriptors for efficient chemical space mapping, development and structural interpretation of machine learning models, and indexing of large databases. - Candida Manelfi; Valerio Tazzari; Filippo Lunghini; Carmen Cerchia; Anna Fava; Alessandro Pedretti; Pieter F. W. Stouten; Giulio Vistoli; Andrea Rosario Beccari (J. Cheminformatics, 2024)

GENEOnet: Statistical analysis supporting explainability and trustworthiness. - Giovanni Bocchi; Patrizio Frosini; Alessandra Micheletti; Alessandro Pedretti; Carmen Gratteri; Filippo Lunghini; Andrea Rosario Beccari; Carmine Talarico (CoRR, 2025)