Table 2.

Sets of HIV-1 PR and RT residue positions used to construct feature vectors

Seta	Description	Positions
All	EC scores at all residue positions in structures for HIV-1 PR (PDB ID: 3phv) and RT (PDB ID: 1rtj, chain A)	PIs: 1 - 99 NRTIs and NNRTIs: 1 - 543
IAS	EC scores only at positions for which residue substitutions occur that are associated with drug resistance.	PIs (common to all: 10, 82, 84, 90) APV: 32, 46, 47, 50, 54, 73, 76 ATV: 16, 20, 24, 32-34, 36, 46, 48, 50, 53, 54, 60, 62, 64, 71, 73, 85, 88, 93 IDV: 20, 24, 32, 36, 46, 54, 71, 73, 76, 77 LPV: 20, 24, 32, 33, 46, 47, 50, 53, 54, 63, 71, 73, 76 NFV: 30, 36, 46, 71, 77, 88 RTV: 20, 32, 33, 36, 46, 54, 71, 77 SQV: 24, 48, 54, 62, 71, 73, 77 TPV: 13, 20, 33, 35, 36, 43, 46, 47, 54, 58, 69, 74, 83 NRTIs (common to all: 41, 67, 70, 210, 215, 219) 3TC: 62, 65, 75, 77, 116, 151, 184 ABC: 62, 65, 74, 75, 77, 115, 116, 151, 184 AZT: 62, 75, 77, 116, 151 d4T: 62, 65, 75, 77, 116, 151 ddC: 62, 65, 69, 74, 75, 77, 116, 151, 184 ddI: 62, 65, 74, 75, 77, 116, 151 FTC: 62, 65, 75, 77, 116, 151, 184 TDF: 65 NNRTIs (common to all: 100, 103, 106, 181, 188, 190) DLV: 230, 236 EFV: 101, 108, 225 NVP: 101, 108
TSM	EC scores only at positions for which residue substitutions occur that are significantly more common in treated versus untreated individuals.	PIs: 10, 11, 20, 23, 24, 30, 32-35, 43, 46-48, 50, 53-55, 58, 66, 67, 71, 73, 74, 76, 79, 82, 84, 85, 88-90, 92, 95 NRTIs: 41, 43, 44, 62, 65, 67, 69, 70, 74, 75, 77, 98, 115, 116, 151, 184, 203, 208, 210, 215, 218, 219, 223, 228 NNRTIs: 100, 101, 103, 106, 108, 138, 181, 188, 190, 221, 225, 227, 230, 236, 238

^a IAS, International Antiviral Society; TSM, nonpolymorphic treatment selected mutations.