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The application discloses a protein-small molecule binding structure prediction method and device, equipment and medium, relates to the technical field of protein-small molecule binding prediction, and includes: obtaining the first modeling graph structure and the second modeling graph structure of the protein block and the small molecule compound to be tested after modeling respectively; inputting the first modeling graph structure and the second modeling graph structure into a TANKBind model to output a predicted protein-small molecule complex through the TANKBind model; generating a first topology file and a second topology file corresponding to a protein structure file and a small molecule structure file of the protein-small molecule complex; performing molecular dynamics simulation by using a preset molecular dynamics simulation tool and a simulation file generated according to the first topology file and the second topology file to obtain a molecular dynamics simulation trajectory file; and analyzing the molecular dynamics simulation trajectory file, the first topology file and the second topology file to obtain simulation analysis results.