The invention provides a method, apparatus, device and storage medium for predicting a protein binding site. The method comprises the steps of: receiving a protein sequence to be predicted, dividing the protein sequence by using a preset sliding window and sliding step to obtain a plurality of amino acid sub-sequences, building word vectors for the protein sequence according to the amino acid sub-sequences, extracting document features from word elements, building document feature vectors for the protein sequence according to the extracted document features, extracting protein chain biological features from the amino acid sub-sequences, building biological feature vectors for the protein sequence according to the extracted biological features, classifying the amino acid sub-sequences expressed with the document feature vectors and the biological feature vectors by using a preset amino acid residue classification model to obtain amino acid residue types for the protein sequence.