Chemoinformatics analysis of protein surface amino acid composition

3rd International Conference on Chemo and BioInformatics, Kragujevac, September 25-26. 2025. (pp. 305-310) 

 

АУТОР(И) / AUTHOR(S): Andrej Milisavljević, Urban Bren, Marko Jukič

 

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DOI:  10.46793/ICCBIKG25.305M

САЖЕТАК / ABSTRACT:

Understanding protein–ligand binding site behavior is central to structure-based drug design. Using the PDBBind+ database, we analyzed the amino acid composition of proteins that have protein–small molecule ligand binding sites, with respect to solvent accessibility and presence of amino acids within binding sites. Tryptophan, Phenylalanine, Tyrosine, Methionine, and Glycine were enriched within solvent-accessible binding regions. The methodology we used is robust, reproducible, and applicable to other, similar, datasets. We extended the analysis to individual taxonomic groups including the human and virus protein subsets, providing insights relevant to the medicinal chemistry community. Composition analysis by protein classification revealed differences in amino acid enrichment across protein types, notably a depletion of cysteine on lyase protein surfaces. We anticipate that these findings will support the creation of future predictive models for use in binding site feature analysis and drug screening across diverse biological targets, advancing binding site prediction and helping accelerate computationally intensive drug discovery within medicinal chemistry.

КЉУЧНЕ РЕЧИ / KEYWORDS:

cheminformatics, protein surface analysis, binding site, small-molecule protein interactions, in-silico drug design

ПРОЈЕКАТ / ACKNOWLEDGEMENT:

Financial resources through the Slovenian Research and Innovation Agency (ARIS) project and program grants P2-0438, I0-E015, P1-0403, Z1-50021, L2-4430, J1-4414, J3-4497, J7-4638, J3-4498, J1-4398, J4-4633, J7-50043, J1-50034, GC-0001, J1-60001, J2-60044, and L7-60161.

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