For better evaluating different algorithms, here, we integrate these three docking benchmarks into one docking benchmark, which includes 107 easy targets, 65 medium targets and 35 difficult targets.

The benchmark can be downloaded from here.
The details of this benchmark is list in xlsx.


An integrated protein-RNA docking benchmark

Targetreceptorreceptor RMSDaligandligand RMSDbinterface RMSDcsourcetypecategory
1ASY_A:R1EOV_A1.52TRA_A4.91.3PRDBunbound-unboundeasy
1AV6_A:B1B42_A0.51AV6_B00.4PRDBunbound-boundeasy
1C9S_L:W2EXT_A0.31C9S_W00.2PRDBunbound-boundeasy
1DDL_ABC:D1AUY_ABC1.11DDL_DE00.6protunboud_modeleasy
1E8O_AB:E1914_AB1.81E8O_E00.6protunboud_modeleasy
1EC6_A:D1DTJ_A1.61EC6_D00.6protunbound-boundeasy
1EFW_A:C1L0W_A1.31C0A_B1.61.1protunboud_modeleasy
1F7Y_A:B2VQE_O0.81DK1_B0.280.59RNAbunbound-unboundeasy
1FFY_A:T1QU3_A1.371QU2_T00.84RNAbunbound-boundeasy
1G2E_A:B4EGL_A0.91G2E_B00.6PRDBunbound-boundeasy
1GAX_B:D1GAX_A0.411IVS_C0.550.43RNAbunbound-unboundeasy
1H4S_AB:T1HC7_AB11H4S_T00.9PRDBunbound-boundeasy
1J1U_A:B1U7D_AB1.31J1U_B00.8PRDBunbound-boundeasy
1JBR_B:D1AQZ_A0.61JBR_D00.5protunbound-boundeasy
1JBS_A:C1AQZ_A0.71Q9A_A3.40.6PRDBunbound-unboundeasy
1K8W_A:B1R3F_A1.91K8W_B01.3PRDBunbound-boundeasy
1KOG_A:I1EVL_A0.61KOG_I00.5protunbound-boundeasy
1KQ2_ABHIKM:R1KQ1_ABHIKM0.61KQ2_R00.5PRDBunbound-boundeasy
1M5O_C:B1OIA_A1.21M5O_B00.9PRDBunbound-boundeasy
1M8V_AM:O1H64_AM0.61M8V_O00.4PRDBunbound-boundeasy
1M8W_A:CE1M8Z_A0.81M8W_CE00.7PRDBunbound-boundeasy
1MJI_A:D1IQ4_A3.21MJI_D01.1protunboud_modeleasy
1N35_A:BC1MUK_A0.51N35_BC00.9PRDBunbound-boundeasy
1N78_A:C1J09_A1.91N78_C01.4PRDBunbound-boundeasy
1QF6_A:B1EVL_A0.81QF6_B00.7PRDBunbound-boundeasy
1S03_H:A1SEI_A1.61S03_A01.5protunboud_modeleasy
1SDS_C:F1XBI_A0.31SDS_F00.4PRDBunbound-boundeasy
1SJ3_P:R1M5O_C0.391VC7_B0.370.38RNAbunbound-unboundeasy
1U0B_B:A1LI5_B0.71U0B_A01PRDBunbound-boundeasy
1U63_A:B1I2A_A1.31U63_B01protunbound-boundeasy
1UVI_A:D1HHS_A0.21UVI_D00.2PRDBunbound-boundeasy
1VFG_B:D4WBY_A1.61VFG_D01.4PRDBunbound-boundeasy
1WNE_A:BC1U09_A0.71WNE_BC00.6PRDBunbound-boundeasy
1WPU_A:C1WPV_A0.21WPU_C00.2PRDBunbound-boundeasy
1WSU_A:E1LVA_A0.72RLU_A4.20.5PRDBunbound-unboundeasy
1YVP_B:EFH1YVR_A1.41YVP_EFH01.3PRDBunbound-boundeasy
1ZBH_AD:E1ZBU_AD0.61JU7_A3.60.6PRDBunbound-unboundeasy
1ZBI_A:CD1ZBF_A0.61ZBI_CD00.6PRDBunbound-boundeasy
2AKE_A:B2DR2_A0.272AZX_C3.30.69RNAbunbound-unboundeasy
2ANR_A:B2ANR_A02ANN_B0.550.25RNAbbound-unboundeasy
2ASB_A:B1K0R_A1.12ASB_B00.8PRDBunbound-boundeasy
2AZ0_AB:CD2B9Z_AB1.32AZ0_CD01PRDBunbound-boundeasy
2AZX_AB:C1R6U_AB0.82AZX_C00.6PRDBunbound-boundeasy
2BGG_A:PQ1W9H_A0.92BGG_PQ00.8PRDBunbound-boundeasy
2BH2_A:C1UWV_A1.41JZX_A9.80.7PRDBunbound-unboundeasy
2BTE_A:B1OBC_A1.22NQP_F4.61.3PRDBunbound-unboundeasy
2BU1_A:R2MS2_A0.22BU1_R00.1protunbound-boundeasy
2CZJ_A:B1WJX_A1.42CZJ_B01.1protunbound-boundeasy
2ERR_A:B2CQ3_A3.42ERR_B00.1protunbound-boundeasy
2EZ6_AB:CD1JFZ_AB12EZ6_CD00.8PRDBunbound-boundeasy
2F8K_A:B2D3D_A0.52F8K_B00.5protunbound-boundeasy
2F8S_AB:CD1YVU_A1.92F8S_CD01.5PRDBunbound-boundeasy
2FK6_A:R1Y44_A0.72FK6_R00.8PRDBunbound-boundeasy
2FMT_A:C1FMT_A1.23CW6_A2.30.9PRDBunbound-unboundeasy
2GIC_A:R2QVJ_A1.32GIC_R00.9PRDBunbound-boundeasy
2GJW_AB:EFH1R0V_AB12GJW_EFH01PRDBunbound-boundeasy
2GXB_A:EF1QGP_A1.12GXB_EF00.7PRDBunbound-boundeasy
2I91_B:EF1YVR_A1.22I91_EF01.4protunbound-boundeasy
2IX1_A:B2IX0_A1.62IX1_B00.9PRDBunbound-boundeasy
2JEA_AB:C2JE6_AB0.32JEA_C00.3PRDBunbound-boundeasy
2QUX_AB:C2QUD_AB0.92QUX_C00.5PRDBunbound-boundeasy
2RFK_A:DE3LWR_A0.973HJY_CD2.581.09RNAbunbound-unboundeasy
2XDB_A:G2XD0_A0.42XDB_G00.32RNAbunbound-boundeasy
2XNR_A:C2XNQ_A12XNR_C01.2PRDBunbound-boundeasy
2ZKO_AB:CD2Z0A_AB0.62ZKO_CD00.8PRDBunbound-boundeasy
2ZNI_AB:C2ZNJ_AB1.462ZNI_D1.071.22RNAbunbound-unboundeasy
2ZUE_A:B2ZUE_A02ZUF_B0.270.13RNAbbound-unboundeasy
3AEV_B:C2E3U_A0.73AEV_C00.5PRDBunbound-boundeasy
3AMT_A:B3AU7_A0.83AMT_B00.7PRDBunbound-boundeasy
3BSB_B:C1M8Z_A1.83BSB_C00.9protunbound-boundeasy
3BSO_A:PT1SH0_A1.33BSO_PT01.5protunbound-boundeasy
3BSX_A:C1M8Z_A1.53BSX_C00.6protunbound-boundeasy
3BX2_A:C3BWT_A0.63BX2_C00.5PRDBunbound-boundeasy
3CIY_A:CD3CIG_A1.23CIY_CD01.4protunbound-boundeasy
3D2S_A:E3D2Q_A0.83D2S_E00.6PRDBunbound-boundeasy
3DD2_H:B1JOU_D0.63DD2_B00.5PRDBunbound-boundeasy
3EPH_A:E3EPK_A0.253EPJ_E0.410.23RNAbunbound-unboundeasy
3EQT_AB:CD2W4R_AD1.23EQT_CD01.2PRDBunbound-boundeasy
3FOZ_A:C2ZXU_A0.532ZM5_C0.710.35RNAbunbound-unboundeasy
3FTE_A:CD3FTD_A1.43FTE_CD01.1PRDBunbound-boundeasy
3HHZ_O:R3PTX_A1.572GIC_R0.970.87RNAbunbound-unboundeasy
3HL2_EAMK:I3BC8_ADGJ0.63RG5_A5.21.3PRDBunbound-unboundeasy
3KS8_AB:EF3KS4_AB0.63KS8_EF00.4PRDBunbound-boundeasy
3LRR_A:CD3LRN_A0.43LRR_CD00.35RNAbunbound-boundeasy
3LWR_ABC:DE3LWP_ABC0.263HJW_DE0.790.39RNAbunbound-unboundeasy
3MDG_AB:C3BAP_AC0.53MDG_C00.9PRDBunbound-boundeasy
3MOJ_B:A2G0C_A13MOJ_A01PRDBunbound-boundeasy
3O8C_A:C3O8B_A13O8C_C01.1PRDBunbound-boundeasy
3OL6_A:BCD1RA6_A0.83OL6_BCD01.1PRDBunbound-boundeasy
3OL9_M:NO3OL6_A0.563OLB_BC0.390.38RNAbunbound-unboundeasy
3OVB_A:C3OV7_A0.333OUY_C0.470.35RNAbunbound-unboundeasy
3PF4_B:R1CSP_A0.53PF4_R00.4PRDBunbound-boundeasy
3QJJ_A:Q3UFC_X13QJJ_Q01PRDBunbound-boundeasy
3RC8_A:E3RC3_A1.13RC8_E00.8PRDBunbound-boundeasy
3VJR_A:B2PTH_A0.81NJM_53.70.8PRDBunbound-unboundeasy
4E78_A:PT4E76_A0.74E78_PT00.8PRDBunbound-boundeasy
4ERD_AB:CD4EYT_AB1.54ERD_CD01.2PRDBunbound-boundeasy
4FVU_A:BC3Q7C_A14FVU_BC00.7PRDBunbound-boundeasy
4ILL_AB:RC4ILR_AB0.94ILL_RC00.9PRDBunbound-boundeasy
4J7M_A:B4J7N_A0.34J7M_B00.3PRDBunbound-boundeasy
4N2Q_A:B4ME2_A2.34N2Q_B01.3PRDBunbound-boundeasy
4YVJ_AB:C3AXZ_AB0.74YVJ_C01.3PRDBunbound-boundeasy
5BUD_A:B5BTH_A0.55BUD_B01.2PRDBunbound-boundeasy
5EIM_A:C5H8A_A0.65EIM_C01.3PRDBunbound-boundeasy
5EX7_A:B4ZLR_A0.45EX7_B00.6PRDBunbound-boundeasy
5F5H_A:C4QI0_A0.55F5H_C00.6PRDBunbound-boundeasy
5HR7_A:D3RFA_A1.45HR7_D01.3PRDBunbound-boundeasy
1C0A_A:B1EQR_A1.61EFW_C1.81.6PRDBunbound-unboundmedium
1CVJ_A:M4F25_A2.71CVJ_M03.9PRDBunbound-boundmedium
1DFU_P:MN1B75_A3364D_CB5.33PRDBunbound-unboundmedium
1DK1_A:B2FKX_A2.81DK1_B02.4protunbound-boundmedium
1E7K_A:C2JNB_A3.21E7K_C01.8protunbound-boundmedium
1EIY_AB:C1JJC_AB1.31EIY_C01.8protunbound-boundmedium
1EKZ_A:B1STU_A5.21EKZ_B03.4protunbound-boundmedium
1F7U_A:B1BS2_A21F7U_B02.2PRDBunbound-boundmedium
1FEU_A:BC2J01_Z2.1364D_BC3.32.4PRDBunbound-unboundmedium
1G1X_A:D1RIS_A1.91G1X_D02.2protunbound-boundmedium
1HC8_A:C1FOY_A2.91HC8_C02.5protunbound-boundmedium
1IL2_A:C1EQR_A1.811ASY_R1.551.7RNAbunbound-unboundmedium
1JID_A:B1JID_A01D4R_A2.64PRDBbound-unboundmedium
1LNG_A:B1LNG_A01Z43_A22.1PRDBbound-unboundmedium
1MFQ_C:A1QB2_B3.11L9A_B5.12.5protunbound-unboundmedium
1MSW_D:R1ARO_P3.51MSW_R03.5PRDBunbound-boundmedium
1Q2R_AB:E1R5Y_AC0.61Q2R_E01.6PRDBunbound-boundmedium
1QTQ_A:B1NYL_A1.63KNH_Y4.81.8PRDBunbound-unboundmedium
1R3E_A:C1ZE1_A21EHZ_A4.93.3PRDBunbound-unboundmedium
1R9F_A:BC1R9F_A03CZ3_EF4.462.1RNAbbound-unboundmedium
1RC7_A:BCDE1YYO_A3.41DI2_CDEF1.083.78RNAbunbound-unboundmedium
1RLG_A:C1XBI_A2.41RLG_C01.6protunboud_modelmedium
1SER_AB:T1SES_AB1.71SER_T02.4PRDBunbound-boundmedium
1T0K_AB:CD1NMU_AB1.51T0K_CD03.3protunbound-boundmedium
1T4L_B:A1T4O_A2.21T4L_A01.7protunbound-boundmedium
1UN6_C:E2HGH_A2.341UN6_F2.572.18RNAbunbound-unboundmedium
2A8V_B:E1A8V_B12A8V_E01.6PRDBunbound-boundmedium
2AD9_A:B1SJQ_A2.92AD9_B02.3protunbound-boundmedium
2ADB_A:B1SJR_A3.72ADB_B02.4protunbound-boundmedium
2ADC_A:B2EVZ_A4.22ADC_B03.7protunbound-boundmedium
2B3J_AB:E1WWR_AB2.22B3J_E02.8protunboud_modelmedium
2CSX_A:C2D5B_A2.22CSX_C02.1protunboud_modelmedium
2D6F_ABCD:E1ZQ1_ABCD2.92D6F_E03.7protunboud_modelmedium
2DER_B:D2HMA_A2.82DER_D03.3protunboud_modelmedium
2DRA_A:B1R89_A1.91VFG_D32.1protunboud_modelmedium
2DRB_A:B1UET_A1.13Q1Q_C3.41.8PRDBunbound-unboundmedium
2DU3_ABCD:EF2DU7_ABCD4.52ZZN_D3.13.7protunboud_modelmedium
2FY1_A:B1X5S_A5.52FY1_B03.1protunboud_modelmedium
2JLU_A:C2JLQ_A2.12JLU_C02.8PRDBunbound-boundmedium
2PJP_A:B2PJP_A01MFK_A2.53.6PRDBbound-unboundmedium
2PY9_B:E2JZX_A1.42PY9_E01.6PRDBunbound-boundmedium
2Q66_A:X2HHP_A1.92Q66_X02.1PRDBunbound-boundmedium
2R7R_A:X2R7Q_A0.22R7R_X01.9PRDBunbound-boundmedium
2R8S_LH:R2HFF_AB1.61HR2_A4.32.9PRDBunbound-unboundmedium
2UWM_A:C1LVA_A7.791WSU_E0.623.19RNAbunbound-unboundmedium
2VPL_A:B2OV7_A1.251U63_B3.681.7RNAbunbound-unboundmedium
2XGJ_A:C4U4C_A4.12XGJ_C03.1PRDBunbound-boundmedium
2Y8W_A:B1WJ9_A1.12Y8W_B03.1PRDBunbound-boundmedium
3ADD_A:C3ADC_A2.633ADB_C0.782.33RNAbunbound-unboundmedium
3BO2_A:BCDE1NU4_A1.73BO2_BCDE01.7protunbound-boundmedium
3BSN_A:PT1SH3_A1.33BSN_PT01.9PRDBunbound-boundmedium
3BT7_A:C3BT7_A01EVV_A3.13.5PRDBbound-unboundmedium
3FTF_A:CD3FTD_A2.413FTE_CD2.332.46RNAbunbound-unboundmedium
3NMR_A:B2DHS_A2.73NMR_B02.2PRDBunbound-boundmedium
3O3I_X:A2L5C_A2.13O3I_A02.7PRDBunbound-boundmedium
3OIJ_AB:C3OII_AB0.83OIJ_C01.7PRDBunbound-boundmedium
3ZJT_A:B3ZJT_A02NQP_F2.82.9PRDBbound-unboundmedium
4H5P_AB:E3LYF_AB0.94H5P_E02.1PRDBunbound-boundmedium
4HOR_A:X4HOQ_A3.14HOR_X02.4PRDBunbound-boundmedium
4IG8_A:BC1PX5_A2.44IG8_BC02.8PRDBunbound-boundmedium
4MDX_AB:C1NE8_AD0.74MDX_C01.6PRDBunbound-boundmedium
4QU6_A:B2LMI_A2.54QU6_B02.4PRDBunbound-boundmedium
5DET_AB:PQ5CYJ_AB1.25DET_PQ01.6PRDBunbound-boundmedium
5ED1_A:BC1ZY7_A1.15ED1_BC02.3PRDBunbound-boundmedium
5ELS_AC:HI5EL3_AB1.55ELS_HI02.9PRDBunbound-boundmedium
1B23_P:R1TUI_A101U0B_A7.213.3PRDBunbound-unbounddifficult
1B7F_A:P3SXL_A6.71B7F_P06.9protunbound-bounddifficult
1FXL_A:B3SXL_A7.41FXL_B07.6protunboud_modeldifficult
1H3E_AD:G1H3F_AB7.71H3E_G04.5PRDBunbound-bounddifficult
1HQ1_A:B1HQ1_A01DUH_A38.330.4PRDBbound-unbounddifficult
1HVU_AB:C2VG5_AB5.41HVU_C06.4protunbound-bounddifficult
1J2B_AB:C1IQ8_AB0.92ZUF_B10.45.5protunboud_modeldifficult
1K1G_A:B2BL5_A10.71K1G_B011.2protunboud_modeldifficult
1MMS_A:C2K3F_A3.53I9C_A1.64.1PRDBunbound-unbounddifficult
1OB2_A:B1EFC_A11.21EHZ_A2.710.6protunbound-unbounddifficult
1OOA_A:C1LE5_B6.22JWV_A6.75.5PRDBunbound-unbounddifficult
1RKJ_A:B2KRR_A10.11QWA_A4.98.3protunboud_modeldifficult
2C0B_ABCD:E2VMK_ABCD19.32C0B_E017.9protunbound-bounddifficult
2CJK_A:B1L3K_A12.82CJK_B013.1protunboud_modeldifficult
2DB3_A:E2I4I_A15.82DB3_E016.5protunboud_modeldifficult
2DLC_AB:Y1N3L_AB6.12DLC_Y04.4protunboud_modeldifficult
2GJE_AD:RS2GIA_AB4.22GJE_RS04.2protunbound-bounddifficult
2HGH_A:B2J7J_A122HGH_B09protunbound-bounddifficult
2HW8_A:B1AD2_A6.72HW8_B05.1PRDBunbound-bounddifficult
2I82_A:E2I82_A03L0U_A4.24.7PRDBbound-unbounddifficult
2IPY_A:C2B3Y_A11.82IPY_C08.4protunboud_modeldifficult
2JPP_AB:C1Y00_AB4.92JPP_C04.2protunboud_modeldifficult
2NUG_A:CDEF1O0W_A14.22NUG_CDEF012protunboud_modeldifficult
2OZB_AB:C2OZB_AB02XEB_AB1112.5PRDBbound-unbounddifficult
2V3C_C:M3DM5_A131Z43_A1.712.5protunboud_modeldifficult
2XZO_A:D2XZP_A6.22XZO_D05PRDBunbound-bounddifficult
2ZM5_A:C2ZM5_A03L0U_A4.26.5PRDBbound-unbounddifficult
2ZZM_A:B2YX1_A15.11WZ2_C4.620PRDBunbound-unbounddifficult
3ADB_A:C3A4M_A22.43ADB_C027.3PRDBunbound-bounddifficult
3IEV_A:D3IEV_A01SDR_B7.68.4PRDBbound-unbounddifficult
3RW6_A:H3RW7_A13.53RW6_H019PRDBunbound-bounddifficult
3SNP_A:C2B3Y_A0.71AQO_A3.814.5PRDBunbound-unbounddifficult
4M59_AB:CD4M57_AB10.54M59_CD07.1PRDBunbound-bounddifficult
4YCP_A:B4BFA_A0.44YCP_B06.8PRDBunbound-bounddifficult
4ZT0_A:B4CMP_A29.64ZT0_B022PRDBunbound-bounddifficult
abcReceptor,ligand or interface rmsd between unbound and bound monomeric structure


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