Cheminformatic analysis of protein surfaces provides binding site insights and informs identification strategies.

ABSTRACT:

Aims

Understanding protein-ligand binding site behavior is central to structure-based drug design. We analyzed amino acid composition and interactions in protein-ligand small-molecule binding sites and developed a novel method for binding site prediction.

Materials and methods

We analyzed the PDBBind+ database, which contains the largest protein-ligand binding site dataset known to us, using existing cheminformatics packages and in-house code. We used the resulting data to train a binding site prediction model.

Results

Within solvent-accessible binding regions, tryptophan, phenylalanine, tyrosine, methionine, and glycine, were enriched. Interaction analysis revealed hydrophobic contacts as the most frequent, followed by hydrogen bonds, water-bridged hydrogen bonds, sa

SUBMITTER: Milisavljevic A 

PROVIDER: S-EPMC12698063 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature