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ORCIDBibTeX records: Walter Rocchia
@article{DBLP:journals/candc/SolerMRF23,
author = {Miguel A. Soler and
Nikola Minovski and
Walter Rocchia and
Sara Fortuna},
title = {Replica-exchange optimization of antibody fragments},
journal = {Comput. Biol. Chem.},
volume = {103},
pages = {107819},
year = {2023},
url = {https://doi.org/10.1016/j.compbiolchem.2023.107819},
doi = {10.1016/J.COMPBIOLCHEM.2023.107819},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/SolerMRF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cg/GagliardiRFBRHA22,
author = {Luca Gagliardi and
Andrea Raffo and
Ulderico Fugacci and
Silvia Biasotti and
Walter Rocchia and
Hao Huang and
Boulbaba Ben Amor and
Yi Fang and
Yuanyuan Zhang and
Xiao Wang and
Charles Christoffer and
Daisuke Kihara and
Apostolos Axenopoulos and
Stelios K. Mylonas and
Petros Daras},
title = {{SHREC} 2022: Protein-ligand binding site recognition},
journal = {Comput. Graph.},
volume = {107},
pages = {20--31},
year = {2022},
url = {https://doi.org/10.1016/j.cag.2022.07.005},
doi = {10.1016/J.CAG.2022.07.005},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cg/GagliardiRFBRHA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cg/RaffoFBRLOZHZPL21,
author = {Andrea Raffo and
Ulderico Fugacci and
Silvia Biasotti and
Walter Rocchia and
Yonghuai Liu and
Ekpo Otu and
Reyer Zwiggelaar and
David Hunter and
Evangelia I. Zacharaki and
Eleftheria Psatha and
Dimitrios Laskos and
Gerasimos Arvanitis and
Konstantinos Moustakas and
Tunde Aderinwale and
Charles Christoffer and
Woong{-}Hee Shin and
Daisuke Kihara and
Andrea Giachetti and
Huu{-}Nghia Nguyen and
Tuan{-}Duy Nguyen and
Vinh{-}Thuyen Nguyen{-}Truong and
Danh Le{-}Thanh and
Hai{-}Dang Nguyen and
Minh{-}Triet Tran},
title = {{SHREC} 2021: Retrieval and classification of protein surfaces equipped
with physical and chemical properties},
journal = {Comput. Graph.},
volume = {99},
pages = {1--21},
year = {2021},
url = {https://doi.org/10.1016/j.cag.2021.06.010},
doi = {10.1016/J.CAG.2021.06.010},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cg/RaffoFBRLOZHZPL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2103-02843,
author = {Agastya P. Bhati and
Shunzhou Wan and
Dario Alf{\`{e}} and
Austin R. Clyde and
Mathis Bode and
Li Tan and
Mikhail Titov and
Andr{\'{e}} Merzky and
Matteo Turilli and
Shantenu Jha and
Roger R. Highfield and
Walter Rocchia and
Nicola Scafuri and
Sauro Succi and
Dieter Kranzlm{\"{u}}ller and
Gerald Mathias and
David Wifling and
Yann Donon and
Alberto Di Meglio and
Sofia Vallecorsa and
Heng Ma and
Anda Trifan and
Arvind Ramanathan and
Tom Brettin and
Alexander Partin and
Fangfang Xia and
Xiaotan Duan and
Rick Stevens and
Peter V. Coveney},
title = {Pandemic Drugs at Pandemic Speed: Accelerating {COVID-19} Drug Discovery
with Hybrid Machine Learning- and Physics-based Simulations on High
Performance Computers},
journal = {CoRR},
volume = {abs/2103.02843},
year = {2021},
url = {https://arxiv.org/abs/2103.02843},
eprinttype = {arXiv},
eprint = {2103.02843},
timestamp = {Mon, 15 Mar 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2103-02843.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/ReisVRM20,
author = {Pedro B. P. S. Reis and
Diogo Vila{-}Vi{\c{c}}osa and
Walter Rocchia and
Miguel Machuqueiro},
title = {PypKa: {A} Flexible Python Module for Poisson-Boltzmann-Based pKa
Calculations},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {10},
pages = {4442--4448},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.0c00718},
doi = {10.1021/ACS.JCIM.0C00718},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/ReisVRM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DecherchiSSR19,
author = {Sergio Decherchi and
Andrea Spitaleri and
John E. Stone and
Walter Rocchia},
title = {NanoShaper-VMD interface: computing and visualizing surfaces, pockets
and channels in molecular systems},
journal = {Bioinform.},
volume = {35},
number = {7},
pages = {1241--1243},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty761},
doi = {10.1093/BIOINFORMATICS/BTY761},
timestamp = {Sat, 07 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DecherchiSSR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cogcom/RagusaGZFRD19,
author = {Edoardo Ragusa and
Paolo Gastaldo and
Rodolfo Zunino and
Marco Jacopo Ferrarotti and
Walter Rocchia and
Sergio Decherchi},
title = {Cognitive Insights into Sentic Spaces Using Principal Paths},
journal = {Cogn. Comput.},
volume = {11},
number = {5},
pages = {656--675},
year = {2019},
url = {https://doi.org/10.1007/s12559-019-09651-1},
doi = {10.1007/S12559-019-09651-1},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cogcom/RagusaGZFRD19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tnn/FerrarottiRD19,
author = {Marco Jacopo Ferrarotti and
Walter Rocchia and
Sergio Decherchi},
title = {Finding Principal Paths in Data Space},
journal = {{IEEE} Trans. Neural Networks Learn. Syst.},
volume = {30},
number = {8},
pages = {2449--2462},
year = {2019},
url = {https://doi.org/10.1109/TNNLS.2018.2884792},
doi = {10.1109/TNNLS.2018.2884792},
timestamp = {Mon, 09 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tnn/FerrarottiRD19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/DecherchiBSRC18,
author = {Sergio Decherchi and
Giovanni Bottegoni and
Andrea Spitaleri and
Walter Rocchia and
Andrea Cavalli},
title = {BiKi Life Sciences: {A} New Suite for Molecular Dynamics and Related
Methods in Drug Discovery},
journal = {J. Chem. Inf. Model.},
volume = {58},
number = {2},
pages = {219--224},
year = {2018},
url = {https://doi.org/10.1021/acs.jcim.7b00680},
doi = {10.1021/ACS.JCIM.7B00680},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/DecherchiBSRC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/DecherchiBSRC18a,
author = {Sergio Decherchi and
Giovanni Bottegoni and
Andrea Spitaleri and
Walter Rocchia and
Andrea Cavalli},
title = {Addendum to BiKi Life Sciences: {A} New Suite for Molecular Dynamics
and Related Methods in Drug Discovery},
journal = {J. Chem. Inf. Model.},
volume = {58},
number = {8},
pages = {1721},
year = {2018},
url = {https://doi.org/10.1021/acs.jcim.8b00489},
doi = {10.1021/ACS.JCIM.8B00489},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/DecherchiBSRC18a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tnn/DecherchiR17,
author = {Sergio Decherchi and
Walter Rocchia},
title = {Import Vector Domain Description: {A} Kernel Logistic One-Class Learning
Algorithm},
journal = {{IEEE} Trans. Neural Networks Learn. Syst.},
volume = {28},
number = {7},
pages = {1722--1729},
year = {2017},
url = {https://doi.org/10.1109/TNNLS.2016.2547220},
doi = {10.1109/TNNLS.2016.2547220},
timestamp = {Mon, 09 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tnn/DecherchiR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1710-03013,
author = {Marco Jacopo Ferrarotti and
Sergio Decherchi and
Walter Rocchia},
title = {Distributed Kernel K-Means for Large Scale Clustering},
journal = {CoRR},
volume = {abs/1710.03013},
year = {2017},
url = {http://arxiv.org/abs/1710.03013},
eprinttype = {arXiv},
eprint = {1710.03013},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1710-03013.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SpyrakisBDRCAOB15,
author = {Francesca Spyrakis and
Paolo Benedetti and
Sergio Decherchi and
Walter Rocchia and
Andrea Cavalli and
Stefano Alcaro and
Francesco Ortuso and
Massimo Baroni and
Gabriele Cruciani},
title = {A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular
Dynamics and Fingerprints for Ligand and Proteins},
journal = {J. Chem. Inf. Model.},
volume = {55},
number = {10},
pages = {2256--2274},
year = {2015},
url = {https://doi.org/10.1021/acs.jcim.5b00169},
doi = {10.1021/ACS.JCIM.5B00169},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/SpyrakisBDRCAOB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ColmenaresOR14,
author = {Jos{\'{e}} Colmenares and
Jes{\'{u}}s Ortiz and
Walter Rocchia},
title = {{GPU} linear and non-linear Poisson-Boltzmann solver module for DelPhi},
journal = {Bioinform.},
volume = {30},
number = {4},
pages = {569--570},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btt699},
doi = {10.1093/BIOINFORMATICS/BTT699},
timestamp = {Tue, 20 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ColmenaresOR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/concurrency/DAgostinoCDRMM14,
author = {Daniele D'Agostino and
Andrea Clematis and
Sergio Decherchi and
Walter Rocchia and
Luciano Milanesi and
Ivan Merelli},
title = {{CUDA} accelerated molecular surface generation},
journal = {Concurr. Comput. Pract. Exp.},
volume = {26},
number = {10},
pages = {1819--1831},
year = {2014},
url = {https://doi.org/10.1002/cpe.3120},
doi = {10.1002/CPE.3120},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/concurrency/DAgostinoCDRMM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/PatelBRRC14,
author = {Jagdish Suresh Patel and
Anna Berteotti and
Simone Ronsisvalle and
Walter Rocchia and
Andrea Cavalli},
title = {Steered Molecular Dynamics Simulations for Studying Protein-Ligand
Interaction in Cyclin-Dependent Kinase 5},
journal = {J. Chem. Inf. Model.},
volume = {54},
number = {2},
pages = {470--480},
year = {2014},
url = {https://doi.org/10.1021/ci4003574},
doi = {10.1021/CI4003574},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/PatelBRRC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pdp/ColmenaresODFR13,
author = {Jos{\'{e}} Colmenares and
Jes{\'{u}}s Ortiz and
Sergio Decherchi and
Amir Fijany and
Walter Rocchia},
title = {Solving the Linearized Poisson-Boltzmann Equation on GPUs Using {CUDA}},
booktitle = {21st Euromicro International Conference on Parallel, Distributed,
and Network-Based Processing, {PDP} 2013, Belfast, United Kingdom,
February 27 - March 1, 2013},
pages = {420--426},
publisher = {{IEEE} Computer Society},
year = {2013},
url = {https://doi.org/10.1109/PDP.2013.67},
doi = {10.1109/PDP.2013.67},
timestamp = {Tue, 20 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/pdp/ColmenaresODFR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ppam/DAgostinoDGCQRC11,
author = {Daniele D'Agostino and
Sergio Decherchi and
Antonella Galizia and
Jos{\'{e}} Colmenares and
Alfonso Quarati and
Walter Rocchia and
Andrea Clematis},
editor = {Roman Wyrzykowski and
Jack J. Dongarra and
Konrad Karczewski and
Jerzy Wasniewski},
title = {{CUDA} Accelerated Blobby Molecular Surface Generation},
booktitle = {Parallel Processing and Applied Mathematics - 9th International Conference,
{PPAM} 2011, Torun, Poland, September 11-14, 2011. Revised Selected
Papers, Part {I}},
series = {Lecture Notes in Computer Science},
volume = {7203},
pages = {347--356},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-31464-3\_35},
doi = {10.1007/978-3-642-31464-3\_35},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ppam/DAgostinoDGCQRC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithms/BonellaRANT09,
author = {Sara Bonella and
Walter Rocchia and
Pietro Amat and
Riccardo Nifos{\'{\i}} and
Valentina Tozzini},
title = {SDPhound, a Mutual Information-Based Method to Investigate Specificity-Determining
Positions},
journal = {Algorithms},
volume = {2},
number = {2},
pages = {764--789},
year = {2009},
url = {https://doi.org/10.3390/a2020764},
doi = {10.3390/A2020764},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/algorithms/BonellaRANT09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/BottegoniRRC06,
author = {Giovanni Bottegoni and
Walter Rocchia and
Maurizio Recanatini and
Andrea Cavalli},
title = {AClAP, Autonomous hierarchical agglomerative Cluster Analysis based
protocol to partition conformational datasets},
booktitle = {Proceedings 14th International Conference on Intelligent Systems for
Molecular Biology 2006, Fortaleza, Brazil, August 6-10, 2006},
pages = {58--65},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl212},
doi = {10.1093/BIOINFORMATICS/BTL212},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/BottegoniRRC06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mcm/Rocchia05,
author = {Walter Rocchia},
title = {Poisson-boltzmann equation boundary conditions for biological applications},
journal = {Math. Comput. Model.},
volume = {41},
number = {10},
pages = {1109--1118},
year = {2005},
url = {https://doi.org/10.1016/j.mcm.2005.05.006},
doi = {10.1016/J.MCM.2005.05.006},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/mcm/Rocchia05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/NeshichRMYKFBPMPKTSTH04,
author = {Goran Neshich and
Walter Rocchia and
Adauto L. Mancini and
Michel E. B. Yamagishi and
Paula R. Kuser and
Renato Fileto and
Christian Baudet and
Ivan P. Pinto and
Arnaldo J. Montagner and
Juliana F. Palandrani and
Jo{\~{a}}o N. Krauchenco and
Renato C. Torres and
Savio Souza and
Roberto C. Togawa and
Roberto H. Higa},
title = {\({}^{\mbox{Java}}\)Protein Dossier: a novel web-based data visualization
tool for comprehensive analysis of protein structure},
journal = {Nucleic Acids Res.},
volume = {32},
number = {Web-Server-Issue},
pages = {595--601},
year = {2004},
url = {https://doi.org/10.1093/nar/gkh480},
doi = {10.1093/NAR/GKH480},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/NeshichRMYKFBPMPKTSTH04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/RocchiaSNACH02,
author = {Walter Rocchia and
Sundaram Sridharan and
Anthony Nicholls and
Emil Alexov and
Alessandro Chiabrera and
Barry Honig},
title = {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},
journal = {J. Comput. Chem.},
volume = {23},
number = {1},
pages = {128--137},
year = {2002},
url = {https://doi.org/10.1002/jcc.1161},
doi = {10.1002/JCC.1161},
timestamp = {Wed, 01 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/RocchiaSNACH02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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