100. Hao G-F, Yang G-F, Zhan C-G (2010) Computational mutation scanning and drug
resistance mechanisms of HIV-1 protease inhibitors. J Phy Chem B 114(29):9663–9676
101. Tse A, Verkhivker GM (2015) Molecular determinants underlying binding specificities of
the ABL kinase inhibitors: combining alanine scanning of binding hot spots with network
analysis of residue interactions and coevolution. PLoS ONE 10(6):e0130203
102. Hou T, Yu R (2007) Molecular dynamics and free energy studies on the wild-type and
double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related
inhibitors: mechanism for binding and drug resistance. J Med Chem 50(6):1177–1188
103. Perryman AL, Lin JH, McCammon JA (2004) HIV-1 protease molecular dynamics of a
wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a
potential new target site for drugs. Protein Sci 13(4):1108–1123
104. Hou T, McLaughlin WA, Wang W (2008) Evaluating the potency of HIV-1 protease drugs
to combat resistance. Proteins: Struct, Funct, Bioinf 71(3):1163–1174
105. Wang W, Kollman PA (2001) Computational study of protein specificity: the molecular
basis of HIV-1 protease drug resistance. Proc Natl Acad Sci USA 98(26):14937–14942
106. Ishikita H, Warshel A (2008) Predicting drug-resistant mutations of HIV protease. Angew
Chem Int Ed 47(4):697–700
107. Singh N, Frushicheva MP, Warshel A (2012) Validating the vitality strategy for fighting
drug resistance. Proteins Struct Funct Bioinf 80(4):1110–1122
24
E. A. F. Martis and E. C. Coutinho
resistance mechanisms of HIV-1 protease inhibitors. J Phy Chem B 114(29):9663–9676
101. Tse A, Verkhivker GM (2015) Molecular determinants underlying binding specificities of
the ABL kinase inhibitors: combining alanine scanning of binding hot spots with network
analysis of residue interactions and coevolution. PLoS ONE 10(6):e0130203
102. Hou T, Yu R (2007) Molecular dynamics and free energy studies on the wild-type and
double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related
inhibitors: mechanism for binding and drug resistance. J Med Chem 50(6):1177–1188
103. Perryman AL, Lin JH, McCammon JA (2004) HIV-1 protease molecular dynamics of a
wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a
potential new target site for drugs. Protein Sci 13(4):1108–1123
104. Hou T, McLaughlin WA, Wang W (2008) Evaluating the potency of HIV-1 protease drugs
to combat resistance. Proteins: Struct, Funct, Bioinf 71(3):1163–1174
105. Wang W, Kollman PA (2001) Computational study of protein specificity: the molecular
basis of HIV-1 protease drug resistance. Proc Natl Acad Sci USA 98(26):14937–14942
106. Ishikita H, Warshel A (2008) Predicting drug-resistant mutations of HIV protease. Angew
Chem Int Ed 47(4):697–700
107. Singh N, Frushicheva MP, Warshel A (2012) Validating the vitality strategy for fighting
drug resistance. Proteins Struct Funct Bioinf 80(4):1110–1122
24
E. A. F. Martis and E. C. Coutinho