Author

Paraskevi Gkeka

Sanofi (France)ORCID 0000-0002-0752-3539Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 4

Signature Assays, Organisms & Methods

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Assay:protein structure· 4 Research Focus:database / resource· 2 Approach:experimental assay· 2 Research Focus:protein structure prediction· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Approach:large language model· 1 Assay:protein sequence· 1

Frequent Co-Authors

Massimiliano BonomiiD· 3 shared Francesco Paolo PaneiiD· 2 shared Hervé MénageriD· 2 shared Matteo MarengoiD· 2 shared Ariadna Montero‐BlayiD· 1 shared Elodie ChapeaublanciD· 1 shared Hervé MinouxiD· 1 shared Laura MaloiD· 1 shared

Activity by Year

2022-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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3 shared papersBioinformatics

Massimiliano BonomiORCID

Mutual co-authors in cluster

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4 papers

Recent·Most cited

HARIBOSS++: An Integrated Platform for RNA-Targeted Drug Design

Matteo Marengo, Elodie Chapeaublanc, Hervé Ménager, Paraskevi Gkeka, Massimiliano Bonomi

HARIBOSS++ is an updated platform for RNA-targeted drug design that includes expanded data and analysis tools for RNA-small molecule interactions.

bioRxiv · Sep 13, 2026 · PreprintBioinformatics

Agent-driven Model Development for RNA 3D Structure Prediction

Maciej Majewski, Laura Malo, Ariadna Montero‐Blay, Matteo Marengo, Ricardo Nascimento Dos Santos, Paraskevi Gkeka, Hervé Minoux

This study uses a large language model agent to iteratively develop an RNA 3D structure prediction model, achieving performance comparable to existing methods at lower cost.

bioRxiv · Sep 10, 2026 · PreprintBioinformatics

Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN

Francesco Paolo Panei, Paraskevi Gkeka, Massimiliano Bonomi

SHAMAN identifies small-molecule binding sites in RNA conformational ensembles using molecular dynamics and enhanced-sampling techniques, successfully detecting experimentally resolved pockets in benchmark tests.

Nature Communications · Jul 8, 2024Peer-reviewedBioinformatics

HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design

Francesco Paolo Panei, Rachel Torchet, Hervé Ménager, Paraskevi Gkeka, Massimiliano Bonomi

HARIBOSS is a curated database of RNA-small molecule structures to support rational drug design by providing insights into RNA-ligand interactions.

Bioinformatics · Jul 7, 2022Peer-reviewedBioinformatics