Patch-Based Ray Tracing in NanoShaper Boosts Molecular Surface Computation.

Walter Rocchia https://zbmath.org/authors/?q=ai:rocchia.walter https://orcid.org/0000-0003-2480-7151 https://www.wikidata.org/entity/Q56904738

Marco Domenico Mazzeo Vincenzo Di Florio Walter Rocchia Sergio Decherchi Patch-Based Ray Tracing in NanoShaper Boosts Molecular Surface Computation. 461-471 2026 66 J. Chem. Inf. Model. 1 https://doi.org/10.1021/acs.jcim.5c02287 db/journals/jcisd/jcisd66.html#MazzeoFRD26 streams/journals/jcisd

Vincenzo Di Florio Patrizio Ansalone Sergii V. Siryk Sergio Decherchi Carlo de Falco Walter Rocchia NextGenPB: An analytically-enabled super resolution tool for solving the Poisson-Boltzmann equation featuring local (de)refinement. 109816 2025 317 Comput. Phys. Commun. https://doi.org/10.1016/j.cpc.2025.109816 db/journals/cphysics/cphysics317.html#FlorioASDFR25 streams/journals/cphysics

Carlo Abate Eleonora Serra Walter Rocchia Andrea Cavalli Sergio Decherchi NanoShaperWeb: Molecular Surface and Pocket Detection Made Visual. 7341-7346 2025 65 J. Chem. Inf. Model. 14 https://doi.org/10.1021/acs.jcim.5c00821 db/journals/jcisd/jcisd65.html#AbateSRCD25 streams/journals/jcisd

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. 55925-55944 2024 12 IEEE Access https://doi.org/10.1109/ACCESS.2024.3389673 db/journals/access/access12.html#BalasubramanianSRDC24

German P. Barletta Rika Tandiana Miguel A. Soler Sara Fortuna Walter Rocchia Locuaz: an <i>in silico</i> platform for protein binders optimization. 2024 40 Bioinform. 8 https://doi.org/10.1093/bioinformatics/btae492 db/journals/bioinformatics/bioinformatics40.html#BarlettaTSFR24

Stefano Bosio Mattia Bernetti Walter Rocchia Matteo Masetti Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin. 4570-4586 2024 64 J. Chem. Inf. Model. 11 https://doi.org/10.1021/acs.jcim.4c00420 db/journals/jcisd/jcisd64.html#BosioBRM24 streams/journals/jcisd

Miguel A. Soler Nikola Minovski Walter Rocchia Sara Fortuna Replica-exchange optimization of antibody fragments. 107819 2023 April 103 Comput. Biol. Chem. https://doi.org/10.1016/j.compbiolchem.2023.107819 db/journals/candc/candc103.html#SolerMRF23

Luca Gagliardi Andrea Raffo Ulderico Fugacci Silvia Biasotti Walter Rocchia Hao Huang 0003 Boulbaba Ben Amor Yi Fang 0006 Yuanyuan Zhang Xiao Wang Charles Christoffer Daisuke Kihara Apostolos Axenopoulos Stelios K. Mylonas Petros Daras SHREC 2022: Protein-ligand binding site recognition. 20-31 2022 107 Comput. Graph. https://doi.org/10.1016/j.cag.2022.07.005 db/journals/cg/cg107.html#GagliardiRFBRHA22

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 0001 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. 1-21 2021 99 Comput. Graph. https://doi.org/10.1016/j.cag.2021.06.010 db/journals/cg/cg99.html#RaffoFBRLOZHZPL21

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. 2021 abs/2103.02843 CoRR https://arxiv.org/abs/2103.02843 db/journals/corr/corr2103.html#abs-2103-02843

Pedro B. P. S. Reis Diogo Vila-Viçosa Walter Rocchia Miguel Machuqueiro PypKa: A Flexible Python Module for Poisson-Boltzmann-Based pKa Calculations. 4442-4448 2020 60 J. Chem. Inf. Model. 10 https://doi.org/10.1021/acs.jcim.0c00718 https://www.wikidata.org/entity/Q98781385 db/journals/jcisd/jcisd60.html#ReisVRM20

Sergio Decherchi Andrea Spitaleri John E. Stone Walter Rocchia NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems. 1241-1243 2019 35 Bioinform. 7 https://doi.org/10.1093/bioinformatics/bty761 https://www.wikidata.org/entity/Q62757938 db/journals/bioinformatics/bioinformatics35.html#DecherchiSSR19

Edoardo Ragusa Paolo Gastaldo Rodolfo Zunino Marco Jacopo Ferrarotti Walter Rocchia Sergio Decherchi Cognitive Insights into Sentic Spaces Using Principal Paths. 656-675 2019 11 Cogn. Comput. 5 https://doi.org/10.1007/s12559-019-09651-1 https://www.wikidata.org/entity/Q127475920 db/journals/cogcom/cogcom11.html#RagusaGZFRD19

Marco Jacopo Ferrarotti Walter Rocchia Sergio Decherchi Finding Principal Paths in Data Space. 2449-2462 2019 30 IEEE Trans. Neural Networks Learn. Syst. 8 https://doi.org/10.1109/TNNLS.2018.2884792 https://www.wikidata.org/entity/Q62757949 db/journals/tnn/tnn30.html#FerrarottiRD19

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. 219-224 2018 58 J. Chem. Inf. Model. 2 https://doi.org/10.1021/acs.jcim.7b00680 https://www.wikidata.org/entity/Q48233999 db/journals/jcisd/jcisd58.html#DecherchiBSRC18

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. 1721 2018 58 J. Chem. Inf. Model. 8 https://doi.org/10.1021/acs.jcim.8b00489 https://www.wikidata.org/entity/Q56340206 db/journals/jcisd/jcisd58.html#DecherchiBSRC18a

Sergio Decherchi Walter Rocchia Import Vector Domain Description: A Kernel Logistic One-Class Learning Algorithm. 1722-1729 2017 28 IEEE Trans. Neural Networks Learn. Syst. 7 https://doi.org/10.1109/TNNLS.2016.2547220 https://www.wikidata.org/entity/Q39839385 db/journals/tnn/tnn28.html#DecherchiR17

Marco Jacopo Ferrarotti Sergio Decherchi Walter Rocchia Distributed Kernel K-Means for Large Scale Clustering. 2017 abs/1710.03013 CoRR http://arxiv.org/abs/1710.03013 db/journals/corr/corr1710.html#abs-1710-03013

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. 2256-2274 2015 55 J. Chem. Inf. Model. 10 https://doi.org/10.1021/acs.jcim.5b00169 https://www.wikidata.org/entity/Q50856972 db/journals/jcisd/jcisd55.html#SpyrakisBDRCAOB15

José Colmenares Jesús Ortiz 0001 Walter Rocchia GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi. 569-570 2014 30 Bioinform. 4 https://doi.org/10.1093/bioinformatics/btt699 https://www.wikidata.org/entity/Q37592026 db/journals/bioinformatics/bioinformatics30.html#ColmenaresOR14

Daniele D'Agostino Andrea Clematis Sergio Decherchi Walter Rocchia Luciano Milanesi Ivan Merelli CUDA accelerated molecular surface generation. 1819-1831 2014 26 Concurr. Comput. Pract. Exp. 10 https://doi.org/10.1002/cpe.3120 https://www.wikidata.org/entity/Q62757969 db/journals/concurrency/concurrency26.html#DAgostinoCDRMM14

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. 470-480 2014 54 J. Chem. Inf. Model. 2 https://doi.org/10.1021/ci4003574 https://www.wikidata.org/entity/Q62757980 db/journals/jcisd/jcisd54.html#PatelBRRC14

José Colmenares Jesús Ortiz 0001 Sergio Decherchi Amir Fijany Walter Rocchia Solving the Linearized Poisson-Boltzmann Equation on GPUs Using CUDA. 420-426 2013 PDP https://doi.org/10.1109/PDP.2013.67 https://doi.ieeecomputersociety.org/10.1109/PDP.2013.67 https://www.wikidata.org/entity/Q62757997 conf/pdp/2013 db/conf/pdp/pdp2013.html#ColmenaresODFR13 Daniele D'Agostino Sergio Decherchi Antonella Galizia José Colmenares Alfonso Quarati Walter Rocchia Andrea Clematis CUDA Accelerated Blobby Molecular Surface Generation. 347-356 2011 PPAM (1) https://doi.org/10.1007/978-3-642-31464-3_35 https://www.wikidata.org/entity/Q62758012 conf/ppam/2011-1 db/conf/ppam/ppam2011-1.html#DAgostinoDGCQRC11

Sara Bonella Walter Rocchia Pietro Amat Riccardo Nifosí Valentina Tozzini SDPhound, a Mutual Information-Based Method to Investigate Specificity-Determining Positions. 764-789 2009 2 Algorithms 2 https://doi.org/10.3390/a2020764 https://www.wikidata.org/entity/Q58022439 db/journals/algorithms/algorithms2.html#BonellaRANT09

Giovanni Bottegoni Walter Rocchia Maurizio Recanatini Andrea Cavalli AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets. 58-65 2006 conf/ismb/2006 ISMB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/btl212 https://www.wikidata.org/entity/Q48437357 db/conf/ismb/ismb2006.html#BottegoniRRC06

Walter Rocchia Poisson-boltzmann equation boundary conditions for biological applications. 1109-1118 2005 41 Math. Comput. Model. 10 https://doi.org/10.1016/j.mcm.2005.05.006 https://www.wikidata.org/entity/Q62758041 db/journals/mcm/mcm41.html#Rocchia05

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 Cristiano Torres Savio Souza Roberto C. Togawa Roberto H. Higa <sup>Java</sup>Protein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. 595-601 2004 32 Nucleic Acids Res. Web-Server-Issue db/journals/nar/nar32.html#NeshichRMYKFBPMPKTSTH04 https://doi.org/10.1093/nar/gkh480 https://www.wikidata.org/entity/Q24562014

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. 128-137 2002 23 J. Comput. Chem. 1 https://doi.org/10.1002/jcc.1161 https://www.wikidata.org/entity/Q29618574 db/journals/jcc/jcc23.html#RocchiaSNACH02

Carlo Abate Tunde Aderinwale Stefano Alcaro Emil Alexov Dario Alfè Pietro Amat Boulbaba Ben Amor Patrizio Ansalone Gerasimos Arvanitis Apostolos Axenopoulos Karthikeyan Kalyanasundaram Balasubramanian German P. Barletta Massimo Baroni Christian Baudet Paolo Benedetti Mattia Bernetti Anna Berteotti Agastya BhatiAgastya P. Bhati Silvia Biasotti Mathis Bode Sara Bonella Stefano Bosio Giovanni Bottegoni Thomas S. BrettinTom Brettin Andrea Cavalli Alessandro Chiabrera Charles Christoffer Andrea Clematis Austin ClydeAustin R. Clyde José Colmenares Peter V. Coveney Marco Crepaldi Gabriele Cruciani Daniele D'Agostino Petros Daras Sergio Decherchi Yann Donon Xiaotian DuanXiaotan Duan Carlo de Falco Yi Fang 0006 Marco Jacopo Ferrarotti Amir Fijany Renato Fileto Vincenzo Di Florio Sara Fortuna Ulderico Fugacci Luca Gagliardi Antonella Galizia Paolo Gastaldo Andrea Giachetti 0001 Roberto H. Higa Roger R. Highfield Barry Honig Hao Huang 0003 David Hunter Shantenu Jha Daisuke Kihara Dieter Kranzlmüller João N. Krauchenco Paula R. Kuser Dimitrios Laskos Danh Le-Thanh Yonghuai Liu Heng Ma Miguel Machuqueiro Adauto L. Mancini Matteo Masetti Gerald Mathias Marco Domenico Mazzeo Alberto Di Meglio Ivan Merelli André Merzky Luciano Milanesi Nikola Minovski Arnaldo J. Montagner Konstantinos Moustakas Stelios K. Mylonas Goran Neshich Hai-Dang Nguyen Huu-Nghia Nguyen Tuan-Duy Nguyen Vinh-Thuyen Nguyen-Truong Anthony Nicholls Riccardo Nifosí Jesús Ortiz 0001 Francesco Ortuso Ekpo Otu Juliana F. Palandrani Alexander Partin Jagdish Suresh Patel Ivan P. Pinto Eleftheria Psatha Alfonso Quarati Andrea Raffo Edoardo Ragusa Arvind Ramanathan Maurizio Recanatini Pedro B. P. S. Reis Simone Ronsisvalle Mirco Di Salvo Nicola Scafuri Eleonora Serra Woong-Hee Shin Sergii V. Siryk Miguel A. Soler Savio Souza Andrea Spitaleri Francesca Spyrakis Sundaram Sridharan Rick L. StevensRick Stevens John E. Stone Sauro Succi Li Tan Rika Tandiana Mikhail Titov Roberto C. Togawa Renato Cristiano Torres Valentina Tozzini Minh-Triet Tran Anda Trifan Matteo Turilli Sofia Vallecorsa Diogo Vila-Viçosa Shunzhou Wan Xiao Wang David Wifling Fangfang Xia Michel Eduardo Beleza YamagishiMichel E. B. Yamagishi Evangelia I. Zacharaki Yuanyuan Zhang Rodolfo Zunino Reyer Zwiggelaar