Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects. - Walter Rocchia; Sundaram Sridharan; Anthony Nicholls; Emil Alexov; Alessandro Chiabrera; Barry Honig (J. Comput. Chem., 2002)

JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. - Goran Neshich; Walter Rocchia; Adauto L. Mancini; Michel E. B. Yamagishi; Paula R. Kuser; Renato Fileto; Christian Baudet; Ivan P. Pinto; Arnaldo J. Montagner; Juliana F. Palandrani; João N. Krauchenco; Renato C. Torres; et al. (Nucleic Acids Res., 2004)

Poisson-boltzmann equation boundary conditions for biological applications. - Walter Rocchia (Math. Comput. Model., 2005)

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)

SDPhound, a Mutual Information-Based Method to Investigate Specificity-Determining Positions. - Sara Bonella; Walter Rocchia; Pietro Amat; Riccardo Nifosí; Valentina Tozzini (Algorithms, 2009)

CUDA Accelerated Blobby Molecular Surface Generation. - Daniele D'Agostino; Sergio Decherchi; Antonella Galizia; José Colmenares; Alfonso Quarati; Walter Rocchia; Andrea Clematis (PPAM (1), 2011)

Solving the Linearized Poisson-Boltzmann Equation on GPUs Using CUDA. - José Colmenares; Jesús Ortiz 001; Sergio Decherchi; Amir Fijany; Walter Rocchia (PDP, 2013)

GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi. - José Colmenares; Jesús Ortiz 001; Walter Rocchia (Bioinform., 2014)

CUDA accelerated molecular surface generation. - Daniele D'Agostino; Andrea Clematis; Sergio Decherchi; Walter Rocchia; Luciano Milanesi; Ivan Merelli (Concurr. Comput. Pract. Exp., 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)

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)

Distributed Kernel K-Means for Large Scale Clustering. - Marco Jacopo Ferrarotti; Sergio Decherchi; Walter Rocchia (CoRR, 2017)

Import Vector Domain Description: A Kernel Logistic One-Class Learning Algorithm. - Sergio Decherchi; Walter Rocchia (IEEE Trans. Neural Networks Learn. Syst., 2017)

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)

NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems. - Sergio Decherchi; Andrea Spitaleri; John E. Stone; Walter Rocchia (Bioinform., 2019)

Cognitive Insights into Sentic Spaces Using Principal Paths. - Edoardo Ragusa; Paolo Gastaldo; Rodolfo Zunino; Marco Jacopo Ferrarotti; Walter Rocchia; Sergio Decherchi (Cogn. Comput., 2019)

Finding Principal Paths in Data Space. - Marco Jacopo Ferrarotti; Walter Rocchia; Sergio Decherchi (IEEE Trans. Neural Networks Learn. Syst., 2019)

PypKa: A Flexible Python Module for Poisson-Boltzmann-Based pKa Calculations. - Pedro B. P. S. Reis; Diogo Vila-Viçosa; Walter Rocchia; Miguel Machuqueiro (J. Chem. Inf. Model., 2020)

SHREC 2021: Retrieval and classification of protein surfaces equipped with physical and chemical properties. - Andrea Raffo; Ulderico Fugacci; Silvia Biasotti; Walter Rocchia; Yonghuai Liu; Ekpo Otu; Reyer Zwiggelaar; David Hunter; Evangelia I. Zacharaki; Eleftheria Psatha; Dimitrios Laskos; Gerasimos Arvanitis; et al. (Comput. Graph., 2021)

Pandemic Drugs at Pandemic Speed: Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers. - Agastya P. Bhati; Shunzhou Wan; Dario Alfè; Austin R. Clyde; Mathis Bode; Li Tan; Mikhail Titov; André Merzky; Matteo Turilli; Shantenu Jha; Roger R. Highfield; Walter Rocchia; et al. (CoRR, 2021)

SHREC 2022: Protein-ligand binding site recognition. - Luca Gagliardi; Andrea Raffo; Ulderico Fugacci; Silvia Biasotti; Walter Rocchia; Hao Huang 003; Boulbaba Ben Amor; Yi Fang 006; Yuanyuan Zhang; Xiao Wang; Charles Christoffer; Daisuke Kihara; et al. (Comput. Graph., 2022)

Replica-exchange optimization of antibody fragments. - Miguel A. Soler; Nikola Minovski; Walter Rocchia; Sara Fortuna (Comput. Biol. Chem., 2023)

Designing RISC-V Instruction Set Extensions for Artificial Neural Networks: An LLVM Compiler-Driven Perspective. - Karthikeyan Kalyanasundaram Balasubramanian; Mirco Di Salvo; Walter Rocchia; Sergio Decherchi; Marco Crepaldi (IEEE Access, 2024)

Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin. - Stefano Bosio; Mattia Bernetti; Walter Rocchia; Matteo Masetti (J. Chem. Inf. Model., 2024)