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Walter Rocchia
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Journal Articles
- 2024
- [j20]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: 55925-55944 (2024) - [j19]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): 4570-4586 (2024) - 2023
- [j18]Miguel A. Soler
, Nikola Minovski
, Walter Rocchia
, Sara Fortuna
:
Replica-exchange optimization of antibody fragments. Comput. Biol. Chem. 103: 107819 (2023) - 2022
- [j17]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: 20-31 (2022) - 2021
- [j16]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: 1-21 (2021) - 2020
- [j15]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): 4442-4448 (2020) - 2019
- [j14]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): 1241-1243 (2019) - [j13]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): 656-675 (2019) - [j12]Marco Jacopo Ferrarotti
, Walter Rocchia
, Sergio Decherchi
:
Finding Principal Paths in Data Space. IEEE Trans. Neural Networks Learn. Syst. 30(8): 2449-2462 (2019) - 2018
- [j11]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): 219-224 (2018) - [j10]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): 1721 (2018) - 2017
- [j9]Sergio Decherchi
, Walter Rocchia
:
Import Vector Domain Description: A Kernel Logistic One-Class Learning Algorithm. IEEE Trans. Neural Networks Learn. Syst. 28(7): 1722-1729 (2017) - 2015
- [j8]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): 2256-2274 (2015) - 2014
- [j7]José Colmenares, Jesús Ortiz
, Walter Rocchia
:
GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi. Bioinform. 30(4): 569-570 (2014) - [j6]Daniele D'Agostino
, Andrea Clematis
, Sergio Decherchi
, Walter Rocchia
, Luciano Milanesi
, Ivan Merelli
:
CUDA accelerated molecular surface generation. Concurr. Comput. Pract. Exp. 26(10): 1819-1831 (2014) - [j5]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): 470-480 (2014) - 2009
- [j4]Sara Bonella
, Walter Rocchia
, Pietro Amat, Riccardo Nifosí, Valentina Tozzini
:
SDPhound, a Mutual Information-Based Method to Investigate Specificity-Determining Positions. Algorithms 2(2): 764-789 (2009) - 2005
- [j3]Walter Rocchia
:
Poisson-boltzmann equation boundary conditions for biological applications. Math. Comput. Model. 41(10): 1109-1118 (2005) - 2004
- [j2]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:
JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. Nucleic Acids Res. 32(Web-Server-Issue): 595-601 (2004) - 2002
- [j1]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): 128-137 (2002)
Conference and Workshop Papers
- 2013
- [c3]José Colmenares, Jesús Ortiz
, Sergio Decherchi
, Amir Fijany, Walter Rocchia
:
Solving the Linearized Poisson-Boltzmann Equation on GPUs Using CUDA. PDP 2013: 420-426 - 2011
- [c2]Daniele D'Agostino
, Sergio Decherchi
, Antonella Galizia
, José Colmenares, Alfonso Quarati
, Walter Rocchia
, Andrea Clematis
:
CUDA Accelerated Blobby Molecular Surface Generation. PPAM (1) 2011: 347-356 - 2006
- [c1]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: 58-65
Informal and Other Publications
- 2021
- [i2]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 abs/2103.02843 (2021) - 2017
- [i1]Marco Jacopo Ferrarotti, Sergio Decherchi, Walter Rocchia:
Distributed Kernel K-Means for Large Scale Clustering. CoRR abs/1710.03013 (2017)
Coauthor Index
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