Table 2 Sets of HIV-1 PR and RT residue positions used to construct feature vectors

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