We　constructed　a　non-redundant　non-ribosomal　protein-RNA　interface　dataset　(including　694　structures)　from　the　Protein　Data　Bank　(PDB).　The　interface　preferences　of　amino　acids,　nucleotides　and　the　secondary　structure　elements　of　protein　and　RNA　were　computed　based　on　the　dataset.　The　results　show　that　beta-ladder,　beta-bridge　and　3(10)-helix　of　proteins　and　the　unpaired　nucleotides　of　RNA,　especially　those　irregularly　arranged　nucleotides　have　remarkably　high　interface　propensities.　Based　on　these,　we　classified　the　secondary　structure　elements,　constructed　the　60x12　amino　acid-nucleotide　pairwise　potential,　and　used　it　as　a　scoring　function　in　protein-RNA　docking　to　select　the　near　native　structures.　The　results　show　the　60x12　pairwise　potential　has　a　scoring　success　rate　of　65.77%,　better　than　those　of　the　pairwise　potentials　with　secondary　structure　information　of　protein　or　RNA　considered,　as　well　as　better　than　that　of　our　previously　constructed　60x　8*　potential　based　on　the　251　protein-RNA　complex　structures.　This　work　is　helpful　for　strengthening　the　understanding　of　protein-RNA　specific　interactions　and　can　advance　the　progress　of　protein-RNA　complex　structure　prediction.