The invention belongs to the technical field of biological information, and provides a protein binding site prediction method, device and equipment and a storage medium. The method comprises the stepsof receiving a protein sequence to be predicted, using a preset sliding window and a sliding step size for performing sequence classification on the protein sequence, obtaining a plurality of amino acid subsequences, constructing a word vector of the protein sequence according to the subsequences, performing document feature extraction on word elements, constructing document feature vectors of the protein sequence according to extracted document features, performing protein chain biological feature extraction on the amino acid subsequences, constructing biological feature vectors of the protein sequence according to the extracted biological features, adopting a preset amino acid residue group classification model for classifying the amino acid subsequences represented by the document feature vectors and the biological feature vectors, and obtaining an amino acid residue group type of the protein sequence; accordingly, the protein binding site prediction accuracy and applicability areimproved.