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. Author manuscript; available in PMC: 2024 Jul 25.
Published in final edited form as: J Chem Inf Model. 2023 Sep 12;63(18):5803–5822. doi: 10.1021/acs.jcim.3c01031

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)
a

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).

b

MAP kinase (1A9U), FGR1 kinase domain (1AGW), COX-1 (1EQH), HMG-CoA reductase (1HW9), HIV reverse transcriptase (1IKW), neuraminidase (3CL0).

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