Table 1.
Primary simulation types employed for D3N growth.
Simulation Type | N Anchors, N Fragments | Main Scoring Function Employed |
---|---|---|
(1) Simple-build (absence of protein) | 380, 382 | Ligand only VDW repulsive term |
(2) Protein-standard (57 systems) a | 15, 382 | Single Grid Energy (SgE) |
(3) Protein-pinpoint (6 systems) b | 380, 382 | Multi Grid Energy (MGE) + Footprint Similarity (FPS) |
acetylcholinesterase (1EVE, 1H22, 1J07, 1Q84, 1ZGC), cyclooxygenase (1EQG, 1EQH, 1HT5, 1HT8, 1Q4G, 4COX), EGFR (2ITP, 2ITT, 2ITY, 2RGP, 3BEL), HIV protease (1AJV, 1DMP, 1HVR, 1MER, 1MES, 1MET, 1QBS, 2F80, 2F81, 2IDW, 2IEN, 2IEO), HIV reverse transcriptase (1C1B, 1C1C, 1VRU, 2BE2, 2RKI, 2ZD1, 3BGR, 3DLE, 3DLG, 3DOL), IGF1R (2ZM3, 3NW5, 3NW6, 3NW7), neuraminidase (1BJI, 1F8B, 1F8C, 1F8D, 1F8E, 1MWE, 1NNB, 1NNC, 1XOE, 1XOG), streptavidin (1DF8, 1SRG, 1SRI, 1SRJ, 2IZL).
MAP kinase (1A9U), FGR1 kinase domain (1AGW), COX-1 (1EQH), HMG-CoA reductase (1HW9), HIV reverse transcriptase (1IKW), neuraminidase (3CL0).