Walter Rocchia

Publication Activity (10 Years)

Years Active: 2002-2024
Publications (10 Years): 14

Top Topics

Protein Sequences

Molecular Dynamics

Top Venues

J. Chem. Inf. Model.

IEEE Trans. Neural Networks Learn. Syst.

Publications

Karthikeyan Kalyanasundaram Balasubramanian, Mirco Di Salvo, Walter Rocchia, Sergio Decherchi, Marco Crepaldi
Designing RISC-V Instruction Set Extensions for Artificial Neural Networks: An LLVM Compiler-Driven Perspective. IEEE Access 12 (2024)
Stefano Bosio, Mattia Bernetti, Walter Rocchia, Matteo Masetti
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin. J. Chem. Inf. Model. 64 (11) (2024)
Miguel A. Soler, Nikola Minovski, Walter Rocchia, Sara Fortuna
Replica-exchange optimization of antibody fragments. Comput. Biol. Chem. 103 (2023)
Luca Gagliardi, Andrea Raffo, Ulderico Fugacci, Silvia Biasotti, Walter Rocchia, Hao Huang, Boulbaba Ben Amor, Yi Fang, Yuanyuan Zhang, Xiao Wang, Charles Christoffer, Daisuke Kihara, Apostolos Axenopoulos, Stelios K. Mylonas, Petros Daras
SHREC 2022: Protein-ligand binding site recognition. Comput. Graph. 107 (2022)
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, Konstantinos Moustakas, Tunde Aderinwale, Charles Christoffer, Woong-Hee Shin, Daisuke Kihara, Andrea Giachetti, Huu-Nghia Nguyen, Tuan-Duy Nguyen, Vinh-Thuyen Nguyen-Truong, Danh Le-Thanh, Hai-Dang Nguyen, Minh-Triet Tran
SHREC 2021: Retrieval and classification of protein surfaces equipped with physical and chemical properties. Comput. Graph. 99 (2021)
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, Nicola Scafuri, Sauro Succi, Dieter Kranzlmüller, Gerald Mathias, David Wifling, Yann Donon, Alberto Di Meglio, Sofia Vallecorsa, Heng Ma, Anda Trifan, Arvind Ramanathan, Tom Brettin, Alexander Partin, Fangfang Xia, Xiaotan Duan, Rick Stevens, Peter V. Coveney
Pandemic Drugs at Pandemic Speed: Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers. CoRR (2021)
Pedro B. P. S. Reis, Diogo Vila-Viçosa, Walter Rocchia, Miguel Machuqueiro
PypKa: A Flexible Python Module for Poisson-Boltzmann-Based pKa Calculations. J. Chem. Inf. Model. 60 (10) (2020)
Sergio Decherchi, Andrea Spitaleri, John E. Stone, Walter Rocchia
NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems. Bioinform. 35 (7) (2019)
Marco Jacopo Ferrarotti, Walter Rocchia, Sergio Decherchi
Finding Principal Paths in Data Space. IEEE Trans. Neural Networks Learn. Syst. 30 (8) (2019)
Edoardo Ragusa, Paolo Gastaldo, Rodolfo Zunino, Marco Jacopo Ferrarotti, Walter Rocchia, Sergio Decherchi
Cognitive Insights into Sentic Spaces Using Principal Paths. Cogn. Comput. 11 (5) (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, 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)
Marco Jacopo Ferrarotti, Sergio Decherchi, Walter Rocchia
Distributed Kernel K-Means for Large Scale Clustering. CoRR (2017)
Sergio Decherchi, Walter Rocchia
Import Vector Domain Description: A Kernel Logistic One-Class Learning Algorithm. IEEE Trans. Neural Networks Learn. Syst. 28 (7) (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)
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)
Daniele D'Agostino, Andrea Clematis, Sergio Decherchi, Walter Rocchia, Luciano Milanesi, Ivan Merelli
CUDA accelerated molecular surface generation. Concurr. Comput. Pract. Exp. 26 (10) (2014)
José Colmenares, Jesús Ortiz, Walter Rocchia
GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi. Bioinform. 30 (4) (2014)
José Colmenares, Jesús Ortiz, Sergio Decherchi, Amir Fijany, Walter Rocchia
Solving the Linearized Poisson-Boltzmann Equation on GPUs Using CUDA. PDP (2013)
Daniele D'Agostino, Sergio Decherchi, Antonella Galizia, José Colmenares, Alfonso Quarati, Walter Rocchia, Andrea Clematis
CUDA Accelerated Blobby Molecular Surface Generation. PPAM (1) (2011)
Sara Bonella, Walter Rocchia, Pietro Amat, Riccardo Nifosí, Valentina Tozzini
SDPhound, a Mutual Information-Based Method to Investigate Specificity-Determining Positions. Algorithms 2 (2) (2009)
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)
Walter Rocchia
Poisson-boltzmann equation boundary conditions for biological applications. Math. Comput. Model. 41 (10) (2005)
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, Savio Souza, Roberto C. Togawa, Roberto H. Higa
Protein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Walter Rocchia, Sundaram Sridharan, Anthony Nicholls, Emil Alexov, Alessandro Chiabrera, Barry Honig
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. J. Comput. Chem. 23 (1) (2002)