Author

Ida de Vries

The Netherlands Cancer InstituteORCID 0000-0002-8313-7779Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Biochemistry· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:benchmarking· 1 Research Focus:database / resource· 1 Organism:human· 1 Assay:protein sequence· 1 Assay:protein structure· 1 Research Focus:protein structure prediction· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Anastassis Perrakis AiD· 3 shared Robbie P. JoosteniD· 2 shared Daniel Álvarez SalmoraliD· 1 shared Georgia Tsiompanaki· 1 shared Jitske BakiD· 1 shared Maarten L. HekkelmaniD· 1 shared Maria Konijnenberg· 1 shared Razvan BorzaiD· 1 shared

Activity by Year

2022-2025 · peak 1/yr

Co-Author Collaboration Network

9 top collaborators · 20 mutual co-author links

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3 shared papersBioinformatics

Anastassis Perrakis AORCID

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3 papers

Recent·Most cited

Halogen bonds between ligands and proteins: can we use them in validation?

Ida de Vries, Georgia Tsiompanaki, Anastassis Perrakis A, Robbie P. Joosten

The paper analyzes halogen bonds in protein-ligand complexes using geometric parameters and introduces a score to assess their validity in structure models from PDB-REDO.

Protein Science · Oct 11, 2025Peer-reviewedBiochemistry

Disentangling the CHAOS of intrinsic disorder in human proteins

Ida de Vries, Jitske Bak, Daniel Álvarez Salmoral, Ren Xie, Razvan Borza, Maria Konijnenberg, Anastassis Perrakis A

The paper develops a comprehensive dataset of intrinsic disorder in human proteins, revealing that most proteins contain disordered regions with distinct characteristics and pathogenic mutation risks.

bioRxiv · Oct 26, 2024 · PreprintBioinformatics

AlphaFill: enriching the AlphaFold models with ligands and co-factors

Maarten L. Hekkelman, Ida de Vries, Robbie P. Joosten, Anastassis Perrakis A

AlphaFill adds missing ligands and cofactors to AlphaFold protein models using sequence and structure similarity to improve functional interpretation.

Nature Methods · Nov 24, 2022Peer-reviewedBioinformatics