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ResearcherID: D-8810-2017
Scopus Author ID: 57193642141

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Czech Republic

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Employment (1)

Charles University: Prague, CZ

2020-01-01 to present (Department of Software Engineering)
Employment
Source: Self-asserted source
Petr Škoda

Education and qualifications (1)

Charles University: Prague, CZ

2014 to 2019 | PhD (Department of Software Engineering)
Education
Source: Self-asserted source
Petr Škoda

Works (35)

Enhancing Domain Modeling with Pre-trained Large Language Models: An Automated Assistant for Domain Modelers

2025 | Book chapter
DOI: 10.1007/978-3-031-75872-0_13
Contributors: Dominik Prokop; Štěpán Stenchlák; Petr Škoda; Jakub Klímek; Martin Nečaský
Source: check_circle
Crossref

Atlas: A Toolset for Efficient Model-Driven Data Exchange in Data Spaces

Proceedings - 2023 ACM/IEEE International Conference on Model Driven Engineering Languages and Systems Companion, MODELS-C 2023
2023 | Conference paper
DOI: 10.1109/MODELS-C59198.2023.00009
EID:

2-s2.0-85182403703

ISBN: 9798350324983
Contributors: Klimek, J.; Koupil, P.; Skoda, P.; Bartik, J.; Stenchlak, S.; Necasky, M.; Holubova, I.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

arXiv
2023 | Other
DOI: 10.48550/arXiv.2309.17255
EID:

2-s2.0-85174561773

Part of ISSN: 23318422
Contributors: Chen, J.; Dong, H.; Hastings, J.; Jiménez-Ruiz, E.; López, V.; Monnin, P.; Pesquita, C.; Škoda, P.; Tamma, V.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

DataSpecer: A Model-Driven Approach to Managing Data Specifications

2022 | Book chapter
DOI: 10.1007/978-3-031-11609-4_10
Contributors: Štěpán Stenchlák; Martin Nečaský; Petr Škoda; Jakub Klímek
Source: check_circle
Crossref
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PDBe-KB: collaboratively defining the biological context of structural data

Nucleic Acids Research
2022 | Journal article
DOI: 10.1093/nar/gkab988
EID:

2-s2.0-85125170185

Part of ISSN: 13624962 03051048
Contributors: Varadi, M.; Anyango, S.; Armstrong, D.; Berrisford, J.; Choudhary, P.; Deshpande, M.; Nadzirin, N.; Nair, S.S.; Pravda, L.; Tanweer, A. et al.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures

Nucleic Acids Research
2022 | Journal article
DOI: 10.1093/nar/gkac389
EID:

2-s2.0-85134384360

Part of ISSN: 13624962 03051048
Contributors: Jakubec, D.; Skoda, P.; Krivak, R.; Novotny, M.; Hoksza, D.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Open dataset discovery using context-enhanced similarity search

Knowledge and Information Systems
2022-12 | Journal article
DOI: 10.1007/s10115-022-01751-z
Contributors: David Bernhauer; Martin Nečaský; Petr Škoda; Jakub Klímek; Tomáš Skopal
Source: check_circle
Crossref
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Modular framework for similarity-based dataset discovery using external knowledge

Data Technologies and Applications
2022-08-23 | Journal article
DOI: 10.1108/DTA-09-2021-0261
Contributors: Martin Nečaský; Petr Škoda; David Bernhauer; Jakub Klímek; Tomáš Skopal
Source: check_circle
Crossref
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Similarity vs. Relevance: From Simple Searches to Complex Discovery

2021 | Book chapter
DOI: 10.1007/978-3-030-89657-7_9
Contributors: Tomáš Skopal; David Bernhauer; Petr Škoda; Jakub Klímek; Martin Nečaský
Source: check_circle
Crossref
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Evaluation Framework for Search Methods Focused on Dataset Findability in Open Data Catalogs

ACM International Conference Proceeding Series
2020 | Conference paper
DOI: 10.1145/3428757.3429973
EID:

2-s2.0-85100331336

ISBN: 9781450389228
Contributors: Škoda, P.; Bernhauer, D.; Nečaský, M.; Klímek, J.; Skopal, T.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Open IE-Triples Inference- Corpora Development and DNN Architectures

Proceedings of the 2020 Federated Conference on Computer Science and Information Systems, FedCSIS 2020
2020 | Conference paper
DOI: 10.15439/2020F78
EID:

2-s2.0-85095775022
Contributors: Vita, M.; Skoda, P.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

PDBE-KB: A community-driven resource for structural and functional annotations

Nucleic Acids Research
2020 | Journal article
DOI: 10.1093/nar/gkz853
EID:

2-s2.0-85075918849

Part of ISSN: 13624962 03051048
Contributors: Varadi, M.; Berrisford, J.; Deshpande, M.; Nair, S.S.; Gutmanas, A.; Armstrong, D.; Pravda, L.; Al-Lazikani, B.; Anyango, S.; Barton, G.J. et al.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Visualizer of Dataset Similarity Using Knowledge Graph

2020 | Book chapter
DOI: 10.1007/978-3-030-60936-8_29
Contributors: Petr Škoda; Jakub Matějík; Tomáš Skopal
Source: check_circle
Crossref
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Preferred source (of 2)‎

Explainable Similarity of Datasets Using Knowledge Graph

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2019 | Conference paper
DOI: 10.1007/978-3-030-32047-8_10
EID:

2-s2.0-85076098613

ISBN: 9783030320461
Part of ISSN: 16113349 03029743
Contributors: Škoda, P.; Klímek, J.; Nečaský, M.; Skopal, T.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

PrankWeb: a web server for ligand binding site prediction and visualization

Nucleic Acids Research
2019 | Journal article
DOI: 10.1093/nar/gkz424
EID:

2-s2.0-85069235250

Part of ISSN: 13624962 03051048
Contributors: Jendele, L.; Krivak, R.; Skoda, P.; Novotny, M.; Hoksza, D.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

PrankWeb: Web server for ligand binding-site prediction and visualization

bioRxiv
2019 | Other
DOI: 10.1101/590877
EID:

2-s2.0-85095638056

Part of ISSN: 26928205
Contributors: Jendele, L.; Krivak, R.; Skoda, P.; Novotny, M.; Hoksza, D.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Software framework for similarity-based prediction of protein interfaces

Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
2019 | Conference paper
DOI: 10.1109/BIBM.2018.8621181
EID:

2-s2.0-85062562218
Contributors: Jelínek, J.; Škoda, P.; Hoksza, D.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Survey of tools for linked data consumption

Semantic Web
2019 | Journal article
DOI: 10.3233/SW-180316
EID:

2-s2.0-85066435278

Part of ISSN: 22104968 15700844
Contributors: Klimek, J.; Skoda, P.; Necasky, M.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Linkedpipes DCAT-AP viewer: A native DCAT-AP data catalog

CEUR Workshop Proceedings
2018 | Conference paper
EID:

2-s2.0-85055315296

Part of ISSN: 16130073
Contributors: Klímek, J.; Škoda, P.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Benchmarking platform for ligand-based virtual screening

Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
2017 | Conference paper
DOI: 10.1109/BIBM.2016.7822693
EID:

2-s2.0-85013313971
Contributors: Skoda, P.; Hoksza, D.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Improving quality of ligand-binding site prediction with Bayesian optimization

Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
2017 | Conference paper
DOI: 10.1109/BIBM.2017.8218024
EID:

2-s2.0-85046003416
Contributors: Krivak, R.; Hoksza, D.; Skoda, P.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

LinkedPipes ETL in use: Practical publication and consumption of Linked Data

ACM International Conference Proceeding Series
2017 | Conference paper
DOI: 10.1145/3151759.3151809
EID:

2-s2.0-85044297727
Contributors: Klímek, J.; Škoda, P.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Platform for ligand-based virtual screening integration

Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
2017 | Conference paper
DOI: 10.1109/BIBM.2017.8218015
EID:

2-s2.0-85045991767
Contributors: Skoda, P.; Hoksza, D.; Jelinek, J.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Practical use cases for linked open data in egovernment demonstrated on the Czech Republic

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2017 | Conference paper
DOI: 10.1007/978-3-319-64248-2_7
EID:

2-s2.0-85028466754

ISBN: 9783319642475
Part of ISSN: 16113349 03029743
Contributors: Nečaský, M.; Klímek, J.; Škoda, P.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Speeding up publication of linked data using data chunking in linkedpipes ETL

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2017 | Conference paper
DOI: 10.1007/978-3-319-69459-7_10
EID:

2-s2.0-85032701073

ISBN: 9783319694580
Part of ISSN: 16113349 03029743
Contributors: Klímek, J.; Škoda, P.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Linkedpipes ETL: Evolved linked data preparation

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2016 | Conference paper
DOI: 10.1007/978-3-319-47602-5_20
EID:

2-s2.0-84994525710

ISBN: 9783319476018
Part of ISSN: 16113349 03029743
Contributors: Klímek, J.; Škoda, P.; Nečaský, M.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier
grade
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Using Bayesian modeling on molecular fragments features for virtual screening

CIBCB 2016 - Annual IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology
2016 | Conference paper
DOI: 10.1109/CIBCB.2016.7758111
EID:

2-s2.0-85011361560
Contributors: Hoksza, D.; Skoda, P.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites

2016 Ieee 6th International Conference on Computational Advances in Bio and Medical Sciences
2016 | Book chapter
WOSUID:

WOS:000392416700016
Contributors: Jelinek, J.; Skoda, P.; Hoksza, D.; Ieee,
Source: Self-asserted source
Petr Škoda via ResearcherID
grade
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Exploration of Topological Torsion Fingerprints

Proceedings 2015 Ieee International Conference on Bioinformatics and Biomedicine
2015 | Book chapter
WOSUID:

WOS:000377335600149
Contributors: Petr, S.; David, H.
Source: Self-asserted source
Petr Škoda via ResearcherID

UnifiedViews: Towards ETL tool for simple yet powerfull RDF data management

CEUR Workshop Proceedings
2015 | Conference paper
EID:

2-s2.0-84930324999
Contributors: Knap, T.; Škoda, P.; Klímek, J.; Nečaský, M.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

2D pharmacophore query generation

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2014 | Conference paper
DOI: 10.1007/978-3-319-08171-7_26
EID:

2-s2.0-84958549180

ISBN: 9783319081700
Part of ISSN: 16113349 03029743
Contributors: Hoksza, D.; Škoda, P.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Molpher: A software framework for systematic chemical space exploration

Journal of Cheminformatics
2014 | Journal article
DOI: 10.1186/1758-2946-6-7
EID:

2-s2.0-84899101876
Contributors: Hoksza, D.; Škoda, P.; Voršilák, M.; Svozil, D.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier
grade
Preferred source (of 2)‎

Scaffold-based chemical space exploration

Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014
2014 | Conference paper
DOI: 10.1109/BIBM.2014.6999387
EID:

2-s2.0-84922822659
Contributors: Hoksza, D.; Škoda, P.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

UnifiedViews: An ETL framework for sustainable RDF data processing

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2014 | Conference paper
DOI: 10.1007/978-3-319-11955-7_52
EID:

2-s2.0-84908680791

ISBN: 9783319119540
Part of ISSN: 16113349 03029743
Contributors: Knap, T.; Kukhar, M.; Macháč, B.; Škoda, P.; Tomeš, J.; Vojt, J.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier

Chemical space visualization using ViFrame

2013 IEEE/ACIS 12th International Conference on Computer and Information Science, ICIS 2013 - Proceedings
2013 | Conference paper
DOI: 10.1109/ICIS.2013.6607895
EID:

2-s2.0-84886573308
Contributors: Skoda, P.; Hoksza, D.
Source: Self-asserted source
Petr Škoda via Scopus - Elsevier
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