MLAFP-XN: Leveraging neural network model for development of antifungal peptide identification tool

Sultan, Md. Fahim; Shaon, Md. Shazzad Hossain; Karim, Tasmin; Ali, Md. Mamun; Hasan, Md. Zahid; Ahmed, Kawsar; Bui, Francis M.; Chen, Li; Dhasarathan, Vigneswaran; Moni, Mohammad Ali

doi:10.1016/j.heliyon.2024.e37820

Heliyon

2024

DOI: 10.1016/j.heliyon.2024.e37820

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MLAFP-XN: Leveraging neural network model for development of antifungal peptide identification tool

Md. Fahim Sultan,

Md. Shazzad Hossain Shaon,

Tasmin Karim

et al.

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2024

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Cited by 1 publication

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AAindexNC: Estimating the Physicochemical Properties of Non-Canonical Amino Acids, Including Those Derived from the PDB and PDBeChem Databank

Milchevskiy,

Kravatskaya,

Kravatsky

2024

IJMS

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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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AAindexNC: Estimating the Physicochemical Properties of Non-Canonical Amino Acids, Including Those Derived from the PDB and PDBeChem Databank

Milchevskiy,

Kravatskaya,

Kravatsky

2024

IJMS

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show abstract

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MLAFP-XN: Leveraging neural network model for development of antifungal peptide identification tool

Cited by 1 publication

References 41 publications

AAindexNC: Estimating the Physicochemical Properties of Non-Canonical Amino Acids, Including Those Derived from the PDB and PDBeChem Databank

AAindexNC: Estimating the Physicochemical Properties of Non-Canonical Amino Acids, Including Those Derived from the PDB and PDBeChem Databank

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