Table 9 Clustering result of docking method showing the PDB IDs for which it performed best during blind docking when top pose was considered
From: Benchmarking of different molecular docking methods for protein-peptide docking
Sr. No. | Docking Method | Number of Complexesa | PDB ID |
|---|---|---|---|
1 | ZDOCK | 30 | 1CJR, 1CKA, 1H6W, 1YMT, 2AQ9, 2CCH, 2D0N, 2DRK, 2FTS, 2HO2, 2P1T, 2VWF, 2WHX, 2XU7, 2ZJD, 3G2S, 3H1Z, 3KMR, 3KUS, 3V2X, 3VTC, 4F1Z, 4J8S, 4K0U, 1RST, 2DYP, 3ASL, 3I5R, 3IVV, 3LL8, |
2 | ATTRACT | 35 | 1D4T, 1JBU, 1NLN, 1PZL, 1QKZ, 1RXZ, 1SFI, 1SSH, 1UJ0, 2A3I, 2B9H, 2BBA, 2FKA, 2HT9, 2O4J, 2PUY, 2V8Y, 3AYU, 3BFQ, 3D32, 3KUJ, 3OLF, 3P8F, 3QIS, 3SFJ, 3SO6, 4E34, 4EIK, 4ERY, 4F14, 4GXL, 4H4F, 2Â CE8, 2VKN, 3ERY |
3 | FRODOCK | 42 | 1MFG, 1NTV, 1NX1, 1OJ5, 1OW6, 1Â T08, 1T4F, 1T7R, 1TFC, 1Â U00, 1YUC, 1YWO, 2FFF, 2FMF, 2O9V, 2P0W, 2P1O, 2P54, 2PEH, 2PUX, 2QOS, 2QSE, 2R7G, 2W2U, 2XRW, 2XVC, 3C3R, 3FDO, 3GYT, 3L0E, 3TZY, 3UP3, 3W1B, 4GYW, 4HTP, 1K5N, 1OU8, 2FFU, 2R9Q, 3OBQ, 3RM1, 3TJV |
4 | PatchDock | 15 | 1HC9, 1X2R, 1XOC, 2O02, 2VR3, 3DS4, 3P72, 3PTL, 3RQG, 4B4N, 4DCB, 4GQ6, 4HOM, 1CVU, 2A25 |
5 | Hex | 8 | 1EG4, 1NQ7, 2FVJ, 2QBX, 3AWR, 3LLZ, 4IIM, 3U9Q |
6 | pepATTRACT | 3 | 1OAI, 3ZQH, 2OEI |