ArticleInternational journal of molecular sciences2024
AAindexNC: Estimating the Physicochemical Properties of Non-Canonical Amino Acids, Including Those Derived from the PDB and PDBeChem Databank.
Article in International journal of molecular sciences, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed.
- TruMPET: A New Method for Protein Secondary Structure Prediction Using Neural Networks Trained on Multiple Pre-Selected Physicochemical and Structural Features.International journal of molecular sciences · 2025Article
- Article
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3 authors.
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Abstract
The physicochemical properties of amino acid residues from the AAindex database are widely used as predictors in building models for predicting both protein structures and properties. It should be noted, however, that the AAindex database contains data only for the 20 canonical amino acids. Non-canonical amino acids, while less common, are not rare; the Protein Data Bank includes proteins with more than 1000 distinct non-canonical amino acids. In this study, we propose a method to evaluate the physicochemical properties from the AAindex database for non-canonical amino acids and assess the prediction quality. We implemented our method as a bioinformatics tool and estimated the physicochemical properties of non-canonical amino acids from the PDB with the chemical composition presentation using SMILES encoding obtained from the PDBechem databank. The bioinformatics tool and resulting database of the estimated properties are freely available on the author's website and available for download via GitHub.
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