Near-Native Selections from Docking Decoys Application to the RosettaDock decoy set Application to ZDOCK2.3 decoy set The EMPIRE score function is tested in the RosettaDock unbound docking decoy set of 54 protein–protein complexes. As in Ref. 41, the selection capability of a score function is characterized by the number of structures within the five lowest energy structures whose root mean squared devia- tion (rmsd) values are less than 10 A˚ from the native com- plex structure (nrmsd). The rmsd value is calculated over the distance deviation of the Ca atoms of the smaller docking partner in the fixed coordinate frame of the larger partner. Gray et al. further defined that a discrimination is successful if nrmsd is greater than or equal to three. Without structural refinement, we find that the success rate based on nrmsd 3 is 37/54 (69%) for EMPIRE, com- pared with 34/54 (63%) for RosettaDock.41 The success rate of EMPIRE, after 50 steps of energy minimization, increases further to 39/54 (72%). It should be noted that without the reference state, the success rate for the direct application of Eq. (2) to RosettaDock decoy sets will be 35/54. Table I compares the performance of the EMPIRE energy function for minimized RosettaDock decoys with that of RosettaDock. There are 21 targets in which EMPIRE has more near-native structures in top 5 than RosettaDock does whereas there are only 10 targets in which RosettaDock has more. The difference illustrates the significant improvement of EMPIRE over RosettaDock. For the ZDOCK set, docking decoys are first refined by sidechain optimization and energy minimization. The refined structures are then ranked according to their re- spective binding affinities calculated by Eq. (3). The per- formance of the proposed refinement and scoring method is measured by success rates. Success rate is defined as per- centage of test cases for which at least one near-native structure has been found within a given number (NP) of lowest-energy structures. Success rates for NP ¼ 1 (top 1) and NP ¼ 10 (top 10) are reported. According to ZDOCK and RDOCK,40,59 a near-native structure is a structure with an interface rmsd of 2.5 A˚ or less. An interface rmsd between a docking decoy and a native complex structure is based on the Ca atoms of interface residues. The value of an interface rmsd is obtained directly from ZDOCK decoy set. We do not recalculate rmsd values. This is because 50 steps of ABNR minimization makes little change in rmsd values and sidechain optimization does not change rmsd values measured by backbone Ca atoms. The result for the ZDOCK 2.3 decoy set is summarized in Table II. It lists the best ranks of near-native structures in ZDOCK2.3 decoy sets along with the number of near- native structures in the 2000 decoys for a given target. Three sets of best ranks are from the application of the EMPIRE function to the original decoys, decoys with side- Table I The Number of Top 5 Decoys with rmsd < 10 A˚ given by EMPIRE and the RosettaDock scoring function 1CGI 1 4 1BRC 5 1 1PPE 5 5 1AHW 0 5 1NMB 5 5 AVZ 0 0 1BTH 0 0 1CHO 5 3 1ACB 3 2 1TAB 5 5 1DQJ 1 2 1MEL 5 5 1MDA 4 3 1FIN 0 0 2PTC 4 2 1BRS 4 4 1UDI 5 5 1BVK 1 5 2VIR 3 4 1IGC 1 2 1FQ1 4 2 1TGS 5 5 1MAH 5 5 1STF 5 5 1FBI 5 3 1EO8 1 1 1ATN 5 5 1GOT 5 0 2SNI 5 4 1UGH 5 5 2TEC 5 5 2JEL 5 5 1QFU 4 5 1GLA 5 1 1EFU 2 0 2SIC 5 5 1DFJ 5 4 4 HTC 5 5 1BQL 2 5 1IAI 3 0 1SPB 5 5 3HHR 2 0 Pdb IDa EMPIREb RosettaDockc Pdb ID EMPIRE RosettaDock Pdb ID EMPIRE RosettaDock Pdb ID EMPIRE RosettaDock Pdb ID EMPIRE RosettaDock Pdb ID EMPIRE RosettaDock Pdb ID EMPIRE RosettaDock DOI 10.1002/prot aEnzyme/Inhibitor: the first 22 protein complexes (1CGI-4HTC); antibody-antigen: the next 16 protein complexes (1MLC-1IAI); the others: (2PCC to 1A0Q); and the difficult set (1BTH to 3HHR). bThis work. cThe high-resolution RosettaDock scoring function.41,71 dThe number of protein-protein complexes with more than 3 near-native structures (rmsd < 10A˚ ) in top 5 ranked decoys. eThe number of near natives given by EMPIRE that is greater than that given by RosettaDock. fThe number of near natives given by RosettaDock that is greater than that given by EMPIRE. 1CSE 5 2 1FSS 3 5 1MLC 2 0 1JHL 1 1 2PCC 4 3 2BTF 3 4 #( 3)d 39 34 2KAI 5 4 1AVW 5 5 1WEJ 2 0 1NQA 5 5 1WQ1 4 3 1A0Q 4 1 #(>) 21e 10f PROTEINS 247