Table 1.
The test set.
| Case1 | UniProt 1 | UniProt 2 | Bound PDB2 | Unbound PDB 13 | Unbound PDB 24 | I-RMSD5 | Docking type |
|---|---|---|---|---|---|---|---|
| 1 Tubulin | β-subunit P04350 | α-subunit P68363 | 4X20 (97%/100%) | 1Z5V (34%) | 1Z5V (32%) | 1.95 (1.88/2.02) [B:A] 2.24 (2.25/2.24) [B:C] | Homology/Homology |
| 2A Succinyl-CoA ligase | α-subunit P53597 | β-subunit Q96I99 | 1EUC (96%/96%) | 1OI7 (54%) | none | 1.02 (1.53/n/a) | Homology/Bound |
| 2B Succinyl-CoA ligase | α-subunit P0AGE9 | β-subunit P0A836 | 1SCU (100%/100%) | 1OI7 (44%) | none | 0.66 (1.02/n/a) | Homology/Bound |
| 2C Succinyl-CoA ligase | α-subunit B7I6T1 | β-subunit B7I6T2 | 1SCU (71%/65%) | 1OI7 (57%) | none | 3.56 (5.19/n/a) | Homology/Bound |
| 2D Succinyl-CoA ligase | α-subunit Q51567 | β-subunit P53593 | 1SCU (89%/77%) | 1OI7 (58%) | none | 2.72 (3.95/n/a) | Homology/Bound |
| 2E Succinyl-CoA ligase | α-subunit Q9WUM5 | β-subunit Q9Z2I8 | 1EUC (94%/93%) | 1OI7 (55%) | none | 1.14 (1.71/n/a) | Homology/Bound |
| 2F Succinyl-CoA ligase | α-subunit Q9WUM5 | β-subunit Q9Z2I9 | 1EUC (94%/55%) | 1OI7 (55%) | none | 1.12 (1.69/n/a) | Homology/Bound |
| 3A F1-ATP synthase | β-subunit P06576 | α-subunit P25705 | 1COW (99%/98%) | 4Q4L (70%) | 2R9V (59%) | 4.72 (5.13/4.29) [A:D] 5.06 (6.05/4.14) [A:E] | Homology/Homology |
| 3B F1-ATP synthase | β-subunit P0ABB4 | α-subunit P0ABB0 | 3OAA (100%/100%) | 4Q4L (80%) | 2R9V (55%) | 4.76 (5.30/4.21) [A:D] 4.79 (5.65/3.87) [A:E] | Homology/Homology |
| 3C F1-ATP synthase | β-subunit P56480 | α-subunit Q03265 | 1COW (98%/98%) | 4Q4L (70%) | 2R9V (60%) | 4.73 (5.17/4.27) [A:D] 5.12 (6.03/4.23) [A:E] | Homology/Homology |
| 4 Profilin-1 β-actin complex | Profilin-1 P07737 | β-actin P60709 | 2BTF (95%/100%) | 1PNE (95%) | 1IJJ (94%) | 0.75 (0.40/0.99) | Unbound/Unbound |
| 5 Alu binding proteins | SRP14 P37108 | SRP9 P49458 | 4UYK (100%/100%) | 2W9J (31%) | none | 1.51 (2.12/n/a) | Homology/Bound |
| 6 Succinate dehydrogenase | Flavoprotein subunit Q8K2B3 | Iron-sulfur subunit Q9CQA3 | 4YXD (94%/92%) | 1KNR (31%) | none | 3.51 (4.65/n/a) | Homology/Bound |
| 7 GTPase | Inhibitor P50395 | Rab14 P61106 | 1UKV (56%/46%) | 1GND (87%) | 4D0G (99%) | 2.20 (1.56/3.02) | Homology/Unbound |
| 8 ElonginB- ElonginC | ElonginC Q15369 | ElonginB Q15370 | 1VCB (100%/100%) | 1HV2 (40%) | none | 1.46 (1.99/n/a) | Homology/Bound |
| 9 BAM complex | BamD P0AC02 | BamC P0A903 | 3TGO (100%/100%) | 3Q5M (100%) | none | 1.36 (1.78/n/a) | Unbound/Bound |
| 10 BAM complex | BamA P0A940 | BamB P77774 | 5D0O (100%/100%) | 5D0Q (100%) | 3Q7N (100%) | 4.42 (5.69/2.69) | Unbound/Unbound |
| 11A BAM complex | BamD P0AC02 | BamA P0A940 | 5D0Q (100%/100%) | 3TGO (100%) | 4K3C (48%) | 2.20 (2.37/1.91) | Unbound/Homology |
| 11B BAM complex | BamD A0A0C2LLC6 | BamA A0A0D8F481 | 5D0Q (36%/35%) | 3TGO (35%) | 4K3C (32%) | 1.86 (2.27/1.05) | Homology/Homology |
1
Human proteins are listed in roman, and other proteins in italic.
2
In parentheses are the sequence identities between the PDB entries and the UniProt sequences in the second and third columns.
3
In parentheses are the sequence identities between the PDB entries and the UniProt 1 sequences in the second column.
4
In parentheses are the sequence identities between the PDB entries and the UniProt 2 sequences in the third column.
5
In parentheses are the I-RMSDs for the two individual proteins. When an unbound structure was not available, the I-RMSD became formally zero and is listed as n/a. I-RMSDs are given for distinct interfaces when present, which are denoted in square brackets.