Due to the current number of experimental analysis of protein-RNA complexes structure rarely,study of protein-RNA interactions and the relationship between the structure and function by molecular docking has important scientific significance and application value[1].In this work,it is mainly to represent how to use molecular docking methods and to predict the protein-RNA complex structure,which relates to two aspects as follows.Based on the study of our group for protein-protein binding site prediction by using PAMA (Product of the solvent accessible Area Multiplies the contact Area) method[2],we modified the PAMA program and extended it to protein-RNA binding site prediction.