Muppirala et al Supplemental Data S2 List of positive RPIs in the RPI369 dataset Protein RNA 1drz_A 1drz_B 2r93_B 2r93_R 2r93_A 2r93_R 1vfg_A 1vfg_C 1jbt_A 1jbt_C 1ec6_B 1ec6_C 1f8v_C 1f8v_R 1f8v_E 1f8v_R 3cw1_G 3cw1_V 3cw1_B 3cw1_V 3cw1_T 3cw1_w 3cw1_P 3cw1_v 3cw1_Y 3cw1_x 3cw1_2 3cw1_x 3cw1_5 3cw1_x 3cw1_K 3cw1_V 3cw1_J 3cw1_x 3cw1_9 3cw1_v 1hq1_A 1hq1_B 1dul_A 1dul_B 2nqp_C 2nqp_F 2az2_A 2az2_C 2hgh_A 2hgh_B 2r92_B 2r92_T 2r92_A 2r92_T 2b2d_C 2b2d_S 2izn_A 2izn_R 1r3e_A 1r3e_E 3ks8_A 3ks8_F 2b2e_C 2b2e_R 2xfz_Y 2xfz_X 2wri_Y 2wri_X 1ze2_B 1ze2_D 1ze2_A 1ze2_C 3mum_P 3mum_R 3mur_P 3mur_R 1x1l_X 1x1l_A 1rpu_B 1rpu_D 2zh4_A 2zh4_B 2ply_A 2ply_C 1wsu_A 1wsu_G 1urn_C 1urn_R 2zh3_A 2zh3_B 2jpp_B 2jpp_D 2wrn_Z 2wrn_Y 3cz3_A 3cz3_E 2cv1_B 2cv1_D 3cz3_B 3cz3_G 1aq4_C 1aq4_S 2c4y_C 2c4y_S 1fje_B 1fje_A 3kfu_H 3kfu_N 3kfu_B 3kfu_N 3kfu_F 3kfu_L 3kfu_G 3kfu_L 1qzw_A 1qzw_B 2dlc_X 2dlc_Y 1zdh_A 1zdh_R 1p6v_C 1p6v_B 2gje_D 2gje_R 2gje_A 2gje_R 2iz8_A 2iz8_R 2wyy_J 2wyy_S 2fk6_A 2fk6_R 1q2r_C 1q2r_F 3deg_C 3deg_G 1a9n_D 1a9n_R 1a9n_A 1a9n_Q 2iy3_A 2iy3_B 2pxv_A 2pxv_B 1urn_A 1urn_P 3htx_D 3htx_E 3ciy_A 3ciy_D 3ktv_B 3ktv_A 2d6f_D 2d6f_F 3hjy_A 3hjy_C 2c50_A 2c50_R 1h3e_A 1h3e_B 1f6u_A 1f6u_B 2j0q_I 2j0q_H 2j0q_B 2j0q_H 1aud_A 1aud_B 1jid_A 1jid_B 1kog_D 1kog_K 1zbh_D 1zbh_F 1q2s_A 1q2s_E 2nuf_A 2nuf_C 2b3j_C 2b3j_G 2xlj_A 2xlj_B 2b2d_C 2b2d_R 2der_B 2der_D 3iab_A 3iab_R 3iab_B 3iab_R 2xli_A 2xli_B 1zdi_A 1zdi_R 3epl_B 3epl_E 2jea_B 2jea_C 2jea_A 2jea_C 1u1y_B 1u1y_S 2csx_A 2csx_D 1ry1_D 1ry1_M 1ry1_C 1ry1_M 5msf_C 5msf_S 3foz_B 3foz_C 1jbr_A 1jbr_C 2fy1_A 2fy1_B 2c4z_A 2c4z_R 1qf6_A 1qf6_B 2ake_A 2ake_B 3ftf_A 3ftf_D 2b9m_Y 2b9m_X 2xlk_B 2xlk_D 2iy5_B 2iy5_T 1eiy_A 1eiy_C 3hl2_B 3hl2_E 1t4l_B 1t4l_A 3cz3_D 3cz3_F 2ob7_B 2ob7_A 1aq3_C 1aq3_R 2izm_C 2izm_S 2c51_C 2c51_S 1j2b_B 1j2b_C 2zh9_A 2zh9_B 3boy_C 3boy_D 5msf_A 5msf_R 2b3j_C 2b3j_H 2az2_B 2az2_D 3iwn_D 3iwn_B 2dra_A 2dra_B 2f8k_A 2f8k_B 1k8w_A 1k8w_B 2izm_C 2izm_R 1u6p_A 1u6p_B 1exd_A 1exd_B 2gjw_C 2gjw_I 3dkn_A 3dkn_F 3akz_B 3akz_E 3al0_B 3al0_E 3al0_C 3al0_E 2bu1_C 2bu1_S 2bs0_C 2bs0_S 2j0s_T 2j0s_E 2j0s_A 2j0s_E 1xok_C 1xok_A 1l1c_A 1l1c_C 2bq5_A 2bq5_R 2pxf_A 2pxf_B 3a2k_B 3a2k_D 2gjw_B 2gjw_E 2ese_A 2ese_B 1aq3_C 1aq3_S 3ivk_B 3ivk_C 2dr5_A 2dr5_B 2oj3_A 2oj3_B 2b63_B 2b63_R 2b63_A 2b63_R 1aq4_A 1aq4_R 1ekz_A 1ekz_B 1zdi_B 1zdi_S 2w2h_A 2w2h_S 2w2h_D 2w2h_S 2jpp_B 2jpp_C 1j1u_A 1j1u_B 1b23_P 1b23_R 1u0b_B 1u0b_A 2nue_B 2nue_C 2nr0_C 2nr0_H 2ez6_A 2ez6_C 1zbh_A 1zbh_E 3d5c_X 3d5c_V 2b6g_A 2b6g_B 3eq4_X 3eq4_Y 2az0_B 2az0_D 1il2_A 1il2_D 1asz_B 1asz_R 1r3e_A 1r3e_C 2b64_Y 2b64_X 1q2s_B 1q2s_F 2pxu_A 2pxu_B 3deg_C 3deg_I 2zh1_A 2zh1_B 2c4z_C 2c4z_S 3a6p_H 3a6p_J 3a6p_F 3a6p_J 2b3j_A 2b3j_F 2b2g_C 2b2g_S 2c4q_C 2c4q_S 2ab4_A 2ab4_B 3dkn_A 3dkn_D 3eq3_X 3eq3_Y 2rfk_A 2rfk_E 2wyy_F 2wyy_R 2bny_B 2bny_R 1m5k_C 1m5k_B 2j28_9 2j28_8 1e8s_B 1e8s_C 1e8s_A 1e8s_C 3k0j_D 3k0j_F 2ozb_D 2ozb_F 2ozb_B 2ozb_C 1r9f_A 1r9f_B 2xb2_T 2xb2_E 2xb2_A 2xb2_E 2drb_A 2drb_B 1ob5_C 1ob5_B 2b2g_C 2b2g_R 2c50_C 2c50_S 2zhb_A 2zhb_B 1urn_B 1urn_Q 3ktw_A 3ktw_C 2du4_A 2du4_C 2dr2_A 2dr2_B 2azx_A 2azx_C 2pxe_A 2pxe_B 2bte_D 2bte_E 2x7n_B 2x7n_A 1u1y_A 1u1y_R 3cz3_D 3cz3_H 2bs1_B 2bs1_R 1rpu_A 1rpu_C 3mr8_V 3mr8_W 3kix_y 3kix_v 3huy_V 3huy_W 2fmt_B 2fmt_C 2xfz_Y 2xfz_V 2wrk_Y 2wrk_V 1sjf_A 1sjf_B 1vbx_A 1vbx_B 1vby_A 1vby_B 2az0_A 2az0_C 2bny_C 2bny_S 2v0g_A 2v0g_F 3id5_A 3id5_D 2anr_A 2anr_B 2pjp_A 2pjp_B 1ser_B 1ser_T 2pxl_A 2pxl_B 1h4s_A 1h4s_T 1hvu_K 1hvu_L 1hvu_A 1hvu_F 1hvu_D 1hvu_C 1rkj_A 1rkj_B 1dz5_A 1dz5_C 2gtt_T 2gtt_X 2bu1_C 2bu1_R 2gtt_D 2gtt_W 2iz9_C 2iz9_R 2pxp_A 2pxp_B 2zzn_A 2zzn_D 1qu3_A 1qu3_T 1r9f_A 1r9f_C 2xlk_A 2xlk_C 1qfq_B 1qfq_A 1efw_B 1efw_D 1c0a_A 1c0a_B 2hvy_A 2hvy_E 2bs0_C 2bs0_R 3hax_A 3hax_E 2f8s_A 2f8s_C 2go5_W 2go5_A 2go5_B 2go5_A 2go5_2 2go5_A 2go5_1 2go5_A 2bx2_L 2bx2_R 1gtn_L 1gtn_W 1gtn_C 1gtn_W 1a1t_A 1a1t_B 1f7u_A 1f7u_B 2bs1_C 2bs1_S 3a6p_C 3a6p_D 3a6p_F 3a6p_I 1gax_A 1gax_C 1zjw_A 1zjw_B 3kiu_y 3kiu_a 3hjy_A 3hjy_D 1r3e_A 1r3e_D 3hhn_D 3hhn_E 3htx_A 3htx_C 2pxt_A 2pxt_B 2i91_B 2i91_F 2zh7_A 2zh7_B 1ec6_A 1ec6_D 1wz2_B 1wz2_D 2zzm_A 2zzm_B 2c51_C 2c51_R 3g8s_D 3g8s_R 2b3j_B 2b3j_E 1lng_A 1lng_B 3dd2_H 3dd2_B 3dd2_L 3dd2_B 2r8s_L 2r8s_R 2pxq_A 2pxq_B 3kis_y 3kis_x 1zdk_B 1zdk_S 2xb2_S 2xb2_R 2xb2_X 2xb2_R 1q2r_D 1q2r_E 2iz8_C 2iz8_S 1ry1_D 1ry1_E 1ry1_C 1ry1_E 2zh2_A 2zh2_B 2ct8_B 2ct8_D 2zh6_A 2zh6_B 1ry1_D 1ry1_N 1ry1_C 1ry1_N 2c4q_B 2c4q_R 1gtf_L 1gtf_W 2b2e_C 2b2e_S 2r92_B 2r92_P 2r92_A 2r92_P 1e7k_B 1e7k_C 1zdk_A 1zdk_R 1mfq_C 1mfq_A 1ry1_W 1ry1_A 1ry1_B 1ry1_A 1l9a_A 1l9a_B 2j37_W 2j37_A 2i91_A 2i91_D 2czj_G 2czj_H 3deg_C 3deg_J 2zh8_A 2zh8_B 3bo3_A 3bo3_B 3hhz_N 3hhz_R 1zse_A 1zse_R 3dkn_A 3dkn_E 2zni_A 2zni_C 2bq5_C 2bq5_S 3egz_A 3egz_B 2zko_A 2zko_C 2zi0_B 2zi0_D 1ooa_A 1ooa_C 1jbr_B 1jbr_D 3foz_B 3foz_D 2iz9_C 2iz9_S 3cun_A 3cun_C 3cul_A 3cul_C 2j0q_T 2j0q_E 2j0q_A 2j0q_E 3ks8_A 3ks8_E 2dr7_A 2dr7_B 2gic_E 2gic_R 2ipy_A 2ipy_D 3icq_C 3icq_E 3icq_U 3icq_E 2rkj_N 2rkj_O 3moj_B 3moj_A 1hji_B 1hji_A 1qrt_A 1qrt_B 1c9s_F 1c9s_W 2v3c_D 2v3c_M 2v3c_A 2v3c_M 2wh1_Y 2wh1_V 2zxu_A 2zxu_C 2ann_A 2ann_B 1zdh_B 1zdh_S 3hay_A 3hay_E 2zuf_A 2zuf_B 2izn_C 2izn_S 3hjw_A 3hjw_D 2c4y_A 2c4y_R 1ttt_B 1ttt_D 1ml5_Z 1ml5_B 3deg_C 3deg_A 1ttt_A 1ttt_D 1sz1_B 1sz1_F 1zo1_I 1zo1_F 3adc_A 3adc_C 2f8t_A 2f8t_D 2ihx_A 2ihx_B