4 papers
PLM-eXplain: Divide and Conquer the Protein Embedding Space
Jan van Eck, Dea Gogishvili, Wilson Silva +1
Protein language models (PLMs) have revolutionised computational biology through their ability to generate powerful sequence representations for diverse prediction tasks. However,…
PatchProt: Hydrophobic patch prediction using protein foundation models
Dea Gogishvili, Emmanuel Minois-Genin, Jan van Eck +1
Hydrophobic patches on protein surfaces play important functional roles in protein-protein and protein-ligand interactions. Large hydrophobic surfaces are also involved in the prog…
Structure Alignment
Olga Ivanova, Jose Gavaldá-Garciá, Dea Gogishvili +4
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book…
How sticky are our proteins? Quantifying hydrophobicity of the human proteome
Juami Hermine Mariama van Gils, Dea Gogishvili, Jan van Eck +3
Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, prot…