Table 3 Related works
Author | Proteins | Drugs | Protein positions | Mutation patterns | Number of sequences | Method |
|---|---|---|---|---|---|---|
Hoffman et al. 2003 [12] | Protease | PI | PR10, PR12, PR13, PR14, | (PR10,PR93) (PR12,PR19) | 1179 | Mutual |
PR15, PR19, PR20, PR30, | (PR35,PR38)(PR63,PR64) | (Subtype B) | information | |||
PR32, PR35, PR36, PR37, | (PR37,PR41)(PR62,PR71) | |||||
PR41, PR46, PR48, PR54, | (PR71,PR77) (PR71,PR93) | |||||
PR57, PR60, PR62, PR63, | (PR77,PR93)(PR12,PR19) | |||||
PR64, PR69, PR71, PR72, | (PR15,PR77)(PR20,PR36) | |||||
PR73, PR77, PR82, PR84, | (PR30,PR88)(PR35,PR36) | |||||
PR88, PR90, PR93 | (PR35,PR37)(PR36,PR62) | |||||
(PR36,PR77)(PR46,PR82) | ||||||
(PR46,PR84)(PR48,PR54) | ||||||
(PR48,PR82)(PR54,PR82) | ||||||
(PR63,PR64)(PR63,PR90) | ||||||
(PR77,PR93)(PR84,PR90) | ||||||
(PR73,PR90) | ||||||
Alteri et al. 2009 [13] | Reverse | PI, | RT41, RT65, RT67, | (RT215,RT41,RT210) | 213 | Binomial |
transcriptase | NRTI, | RT69, RT70, RT74, RT75, | (RT60,RT103) | (Subtype B) | correlation | |
NNRTI | RT77, RT100, RT101, | coefficient, | ||||
RT103, RT106, RT115, | Benjamini- | |||||
RT116, RT151, RT181, | Hochberg | |||||
RT184,RT188, RT190, | method | |||||
RT210, RT215, RT219, | ||||||
RT225, RT230, RT236, | ||||||
Doherty et al. 2011 [14] | Protease | PI | PR10, PR24, PR30, | (PR10,PR32,PR33, | 398 | Optimal |
PR32, PR33, PR43, | PR46,PR47,PR54, | integer | ||||
PR46, PR47, PR48, | PR71,PR73,PR84,PR90) | programming- | ||||
PR50, PR53, PR54, | (PR10,PR33,PR43,PR46, | based | ||||
PR71, PR73, PR74, | PR54,PR71,PR82,PR84,PR90) | clustering | ||||
PR76, PR82, PR83, | (PR10,PR24,PR46, | |||||
PR84, PR88, PR90 | PR54,PR71,PR74,PR82) | |||||
(PR32,PR33,PR46,PR53, | ||||||
PR54,PR71,PR84,PR90) | ||||||
(PR10,PR30,PR32,PR33,PR46, | ||||||
PR54,PR71,PR84,PR88,PR90) | ||||||
(PR10,PR33,PR43,PR46,PR48, | ||||||
PR50,PR54,PR71,PR82) | ||||||
(PR10,PR32,PR46, | ||||||
PR71,PR82,PR84) | ||||||
(PR10,PR46,PR54,PR82,PR90) | ||||||
(PR10,PR48,PR54,PR71, | ||||||
PR73,PR76,PR84,PR90) | ||||||
(PR10,PR24,PR32,PR33, PR43, | ||||||
PR46,PR54,PR71,PR82,PR84) | ||||||
(PR10,PR24,PR30, | ||||||
PR33,PR43,PR53,PR88) | ||||||
(PR10,PR43,PR47,PR48, | ||||||
PR53,PR54,PR71,PR82,PR84) | ||||||
(PR10,PR32,PR46, | ||||||
PR47,PR71,PR82,PR90) | ||||||
(PR10,PR33,PR54, | ||||||
PR73,PR84,PR90) | ||||||
(PR10,PR46,PR71,PR84,PR90) | ||||||
(PR10,PR54,PR71, | ||||||
PR73,PR82,PR90) | ||||||
(PR10,PR32,PR33, | ||||||
PR47,PR71,PR82,PR90) | ||||||
(PR10,PR46,PR54, | ||||||
PR71,PR82,PR90) | ||||||
(PR10,PR24,PR33,PR46, | ||||||
PR54,PR71,PR82) | ||||||
(PR10,PR48,PR54,PR82,PR90) | ||||||
(PR10,PR32,PR43, | ||||||
PR46,PR47,PR82) | ||||||
(PR10,PR54,PR71,PR82) | ||||||
(PR10,PR46,PR47, | ||||||
PR71,PR88,PR90) | ||||||
(PR10,PR33,PR43,PR46, | ||||||
PR50,PR54,PR71, | ||||||
PR73,PR82,PR90) | ||||||
(PR10,PR33,PR46, | ||||||
PR54,PR71,PR88,PR90) | ||||||
(PR10,PR46,PR71, | ||||||
PR74,PR88,PR90) | ||||||
(PR10,PR54,PR74,PR76,PR82) | ||||||
(PR73,PR90) | ||||||
(PR10,PR46,PR90) | ||||||
(PR10,PR71,PR90) | ||||||
(PR10,PR46,PR71) | ||||||
(PR10,PR24,PR46,PR54,PR82) | ||||||
Heider et al. 2013 [15] | Reverse | NRTI | RT1 to RT240 | (RT41,RT70, | 600 | Multilabel |
transcriptase | RT210,RT215) | (Subtype B) | classification | |||
(RT41,RT65,RT67, | ||||||
RT70,RT210,RT215,RT219) | ||||||
(RT65,RT74,RT115) | ||||||
(RT151,RT62,RT69, | ||||||
RT75,RT77,RT116) | ||||||
Yahi et al. 1999 [16] | Protease | PI, | PR63, PR77,PR71, | (PR10,PR46) (PR46,PR71) | 287 | Chi-square |
and | NRTI, | PR10, PR93, PR 36 | (PR46,PR90) (PR71,PR82) | or Kendall | ||
Reverse | NNRTI | PR82, PR46, PR20, | (PR10,PR82) (PR54,PR82) | and | ||
transcriptase | PR90 and PR54 | (PR82,PR90) (PR71,PR90) | Fisher’s | |||
RT215, RT41, RT67, | (PR10,PR90) (PR46,PR90) | two-tailed | ||||
RT69, RT70, RT184, | (PR54,PR90) (PR77,PR90) | |||||
RT210 and RT219 | (PR82,PR90) | |||||
(RT41,RT210) (RT67,RT70) | ||||||
(RT69,RT70) (RT70,RT219) | ||||||
(RT41,RT210) (RT184,RT210) | ||||||
(RT210,RT215) (RT70,RT219) | ||||||
(RT67,RT219) (RT69,RT219) | ||||||
Melikian et al. 2013 [28] | Reverse | NNRTI | (RT101,RT103,RT106, | 1752 | Least | |
transcriptase | RT181,RT188,RT190) | (1681 | angle | |||
(RT100,RT101,RT103, | Subtype B) | regression | ||||
RT106,RT188,RT190) | (LARS) | |||||
(RT101,RT181,RT190,RT227) | ||||||
(RT100,RT101,RT181, | ||||||
RT190,RT227) |