Mgr. Eva Maršálková, Ph.D.

2026

• AlphaFind v2: similarity search in AlphaFold DB and TED domains across structural contexts

  SLANINÁKOVÁ Terézia ROŠINEC Adrián ČILLÍK Jakub KŘENEK Aleš GREŠOVÁ Katarína PORUBSKÁ Jana MARŠÁLKOVÁ Eva OĽHA Jaroslav PROCHÁZKA David HEJTMÁNEK Lukáš DOHNAL Vlastislav BERKA Karel SVOBODOVÁ Radka ANTOL Matej

  Peer-reviewed scientific article

  NUCLEIC ACIDS RESEARCH, year: 2026, DOI

• AlphaFind v2: Similarity Search in AlphaFold DB and TED Domains across Structural Contexts - data

  SLANINÁKOVÁ Terézia ROŠINEC Adrián ČILLÍK Jakub KŘENEK Aleš GREŠOVÁ Katarína PORUBSKÁ Jana MARŠÁLKOVÁ Eva OĽHA Jaroslav PROCHÁZKA David HEJTMÁNEK Lukáš DOHNAL Vlastislav BERKA Karel SVOBODOVÁ Radka ANTOL Matej

  Specialized public database

  Year: 2026, type: Specialized public database, DOI

• Balancing speed and precision in protein folding: a comparison of AlphaFold2, ESMFold, and OmegaFold

  HÝSKOVÁ Anna MARŠÁLKOVÁ Eva ŠIMEČEK Petr

  Peer-reviewed scientific article

  Frontiers in Genetics, year: 2026, volume: 16, edition: January, DOI

2025

• miRBench: novel benchmark datasets for microRNA binding site prediction that mitigate against prevalent microRNA frequency class bias

  SAMMUT Stephanie GREŠOVÁ Katarína TZIMOTOUDIS Dimosthenis MARŠÁLKOVÁ Eva ČECHÁK David ALEXIOU Panagiotis

  Peer-reviewed scientific article

  Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference, year: 2025, volume: 41, edition: 1, DOI

• Refining Structure-Based Search in AlphaFold DB: Including confidence metrics into AlphaFind

  SLANINÁKOVÁ Terézia MARŠÁLKOVÁ Eva GREŠOVÁ Katarína KŘENEK Aleš OĽHA Jaroslav PAVLÍK Tomáš ŠPRINGEROVÁ Pavlína SEHNAL David ANTOL Matej

  Conference abstract

  Year: 2025, type: Conference abstract, DOI

2024

• Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model

  SIKORA Maciej KLIMENTOVÁ Eva UCHAL Dawid ŠRÁMKOVÁ Denisa PERLINSKA Agata P NGUYEN Mai Lan KORPACZ Marta MALINOWSKA Roksana NOWAKOWSKI Szymon RUBACH Pawel ŠIMEČEK Petr SULKOWSKA Joanna I

  Peer-reviewed scientific article

  Protein Science, year: 2024, volume: 33, edition: 7, DOI

2023

• Analysis of chimeric reads characterises the diverse targetome of AGO2-mediated regulation

  HEJRET Václav VARADARAJAN Nandan Mysore KLIMENTOVÁ Eva GREŠOVÁ Katarína GIASSA Ilektra-Chara VAŇÁČOVÁ Štěpánka ALEXIOU Panagiotis

  Peer-reviewed scientific article

  Scientific Reports, year: 2023, volume: 13, edition: 1, DOI

• The SAP domain of Ku facilitates its efficient loading onto DNA ends

  FULNEČEK Jaroslav KLIMENTOVÁ Eva CAIRO CALZADA Albert BUKOVČÁKOVÁ Soňa ALEXIOU Panagiotis PROKOP Zbyněk ŘÍHA Karel

  Peer-reviewed scientific article

  Nucleic Acids Research, year: 2023, volume: 51, edition: 21, DOI

2022

• miRBind: a Deep Learning method for miRNA binding classification

  KLIMENTOVÁ Eva HEJRET Václav GREŠOVÁ Katarína GIASSA Ilektra-Chara ALEXIOU Panagiotis

  Conference abstract

  Year: 2022, type: Conference abstract

• miRBind: A Deep Learning Method for miRNA Binding Classification

  KLIMENTOVÁ Eva HEJRET Václav KRČMÁŘ Ján GREŠOVÁ Katarína GIASSA Ilektra-Chara ALEXIOU Panagiotis

  Peer-reviewed scientific article

  GENES, year: 2022, volume: 13, edition: 12, DOI