-
1
-
-
1842839788
-
Simulating protein evolution in sequence and structure space
-
Xia Y, Levitt M, (2004) Simulating protein evolution in sequence and structure space. Curr Opin Struct Biol 14: 202-207.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 202-207
-
-
Xia, Y.1
Levitt, M.2
-
2
-
-
33645811495
-
Protein stability promotes evolvability
-
Bloom JD, Labthavikul ST, Otey CR, Arnold FH, (2006) Protein stability promotes evolvability. Proc Natl Acad Sci U S A 103: 5869-5874.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 5869-5874
-
-
Bloom, J.D.1
Labthavikul, S.T.2
Otey, C.R.3
Arnold, F.H.4
-
3
-
-
14144251690
-
Thermodynamic prediction of protein neutrality
-
Bloom JD, Silberg JJ, Wilke CO, Drummond DA, Adami C, et al. (2005) Thermodynamic prediction of protein neutrality. Proc Natl Acad Sci U S A 102: 606-611.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 606-611
-
-
Bloom, J.D.1
Silberg, J.J.2
Wilke, C.O.3
Drummond, D.A.4
Adami, C.5
-
5
-
-
34248674895
-
The stability effects of protein mutations appear to be universally distributed
-
Tokuriki N, Stricher F, Schymkowitz J, Serrano L, Tawfik DS, (2007) The stability effects of protein mutations appear to be universally distributed. J Mol Biol 369: 1318-1332.
-
(2007)
J Mol Biol
, vol.369
, pp. 1318-1332
-
-
Tokuriki, N.1
Stricher, F.2
Schymkowitz, J.3
Serrano, L.4
Tawfik, D.S.5
-
6
-
-
33746639718
-
Emergence of protein fold families through rational design
-
Ding F, Dokholyan NV, (2006) Emergence of protein fold families through rational design. PLoS Comput Biol 2: e85.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Ding, F.1
Dokholyan, N.V.2
-
7
-
-
54749086397
-
A specificity map for the PDZ domain family
-
Tonikian R, Zhang Y, Sazinsky SL, Currell B, Yeh J-H, et al. (2008) A specificity map for the PDZ domain family. PLoS Biol 6: e239.
-
(2008)
PLoS Biol
, vol.6
-
-
Tonikian, R.1
Zhang, Y.2
Sazinsky, S.L.3
Currell, B.4
Yeh, J.-H.5
-
8
-
-
11244281311
-
The 'evolvability' of promiscuous protein functions
-
Aharoni A, Gaidukov L, Khersonsky O, McQ Gould S, Roodveldt C, et al. (2005) The 'evolvability' of promiscuous protein functions. Nat Genet 37: 73-76.
-
(2005)
Nat Genet
, vol.37
, pp. 73-76
-
-
Aharoni, A.1
Gaidukov, L.2
Khersonsky, O.3
McQ Gould, S.4
Roodveldt, C.5
-
9
-
-
56149121547
-
Directed enzyme evolution via small and effective neutral drift libraries
-
Gupta RD, Tawfik DS, (2008) Directed enzyme evolution via small and effective neutral drift libraries. Nat Methods 5: 939-942.
-
(2008)
Nat Methods
, vol.5
, pp. 939-942
-
-
Gupta, R.D.1
Tawfik, D.S.2
-
10
-
-
34548383489
-
Design of multi-specificity in protein interfaces
-
Humphris EL, Kortemme T, (2007) Design of multi-specificity in protein interfaces. PLoS Comput Biol 3: e164.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Humphris, E.L.1
Kortemme, T.2
-
11
-
-
33745229352
-
Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily
-
Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, et al. (2006) Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily. J Mol Biol 360: 228-250.
-
(2006)
J Mol Biol
, vol.360
, pp. 228-250
-
-
Glasner, M.E.1
Fayazmanesh, N.2
Chiang, R.A.3
Sakai, A.4
Jacobson, M.P.5
-
12
-
-
16844379112
-
Directed evolution of the promiscuous esterase activity of carbonic anhydrase II
-
Gould SM, Tawfik DS, (2005) Directed evolution of the promiscuous esterase activity of carbonic anhydrase II. Biochemistry 44: 5444-5452.
-
(2005)
Biochemistry
, vol.44
, pp. 5444-5452
-
-
Gould, S.M.1
Tawfik, D.S.2
-
13
-
-
0028952146
-
HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy
-
Coffin JM, (1995) HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 267: 483-489.
-
(1995)
Science
, vol.267
, pp. 483-489
-
-
Coffin, J.M.1
-
14
-
-
0038192438
-
Experimental prediction of the evolution of cefepime resistance from the CMY-2 AmpC beta-lactamase
-
Barlow M, Hall BG, (2003) Experimental prediction of the evolution of cefepime resistance from the CMY-2 AmpC beta-lactamase. Genetics 164: 23-29.
-
(2003)
Genetics
, vol.164
, pp. 23-29
-
-
Barlow, M.1
Hall, B.G.2
-
15
-
-
0037250521
-
Human immunodeficiency virus reverse transcriptase and protease sequence database
-
Rhee S-Y, Gonzales MJ, Kantor R, Betts BJ, Ravela J, et al. (2003) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res 31: 298-303.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 298-303
-
-
Rhee, S.-Y.1
Gonzales, M.J.2
Kantor, R.3
Betts, B.J.4
Ravela, J.5
-
16
-
-
0024406911
-
Complete mutagenesis of the HIV-1 protease
-
Loeb DD, Swanstrom R, Everitt L, Manchester M, Stamper SE, et al. (1989) Complete mutagenesis of the HIV-1 protease. Nature 340: 397-400.
-
(1989)
Nature
, vol.340
, pp. 397-400
-
-
Loeb, D.D.1
Swanstrom, R.2
Everitt, L.3
Manchester, M.4
Stamper, S.E.5
-
17
-
-
0345306764
-
Design of a novel globular protein fold with atomic-level accuracy
-
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, et al. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302: 1364-1368.
-
(2003)
Science
, vol.302
, pp. 1364-1368
-
-
Kuhlman, B.1
Dantas, G.2
Ireton, G.C.3
Varani, G.4
Stoddard, B.L.5
-
18
-
-
57049180165
-
Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design
-
Humphris EL, Kortemme T, (2008) Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design. Structure 16: 1777-1788.
-
(2008)
Structure
, vol.16
, pp. 1777-1788
-
-
Humphris, E.L.1
Kortemme, T.2
-
19
-
-
67049155677
-
A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family
-
Friedland GD, Lakomek N-A, Griesinger C, Meiler J, Kortemme T, (2009) A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol 5: e1000393.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Friedland, G.D.1
Lakomek, N.-A.2
Griesinger, C.3
Meiler, J.4
Kortemme, T.5
-
20
-
-
45649084560
-
Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction
-
Smith CA, Kortemme T, (2008) Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol 380: 742-756.
-
(2008)
J Mol Biol
, vol.380
, pp. 742-756
-
-
Smith, C.A.1
Kortemme, T.2
-
21
-
-
0036298514
-
Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility
-
Zoete V, Michielin O, Karplus M, (2002) Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility. J Mol Biol 315: 21-52.
-
(2002)
J Mol Biol
, vol.315
, pp. 21-52
-
-
Zoete, V.1
Michielin, O.2
Karplus, M.3
-
22
-
-
79960609097
-
Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design
-
Smith CA, Kortemme T, (2011) Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design. PLoS One 6: e20451.
-
(2011)
PLoS One
, vol.6
-
-
Smith, C.A.1
Kortemme, T.2
-
23
-
-
59849127268
-
Update of the Drug Resistance Mutations in HIV-1
-
Johnson VA, Brun-Vezinet F, Clotet B, Gunthard HF, Kuritzkes DR, et al. (2008) Update of the Drug Resistance Mutations in HIV-1. Top HIV Med 16: 138-145.
-
(2008)
Top HIV Med
, vol.16
, pp. 138-145
-
-
Johnson, V.A.1
Brun-Vezinet, F.2
Clotet, B.3
Gunthard, H.F.4
Kuritzkes, D.R.5
-
24
-
-
22544486548
-
HIV-1 Protease and reverse-transcriptase mutations: correlations with antiretroviral therapy in subtype B isolates and implications for drug-resistance surveillance
-
Rhee S-Y, Fessel WJ, Zolopa AR, Hurley L, Liu T, et al. (2005) HIV-1 Protease and reverse-transcriptase mutations: correlations with antiretroviral therapy in subtype B isolates and implications for drug-resistance surveillance. J Infect Dis 192: 456-465.
-
(2005)
J Infect Dis
, vol.192
, pp. 456-465
-
-
Rhee, S.-Y.1
Fessel, W.J.2
Zolopa, A.R.3
Hurley, L.4
Liu, T.5
-
25
-
-
62749200513
-
Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update
-
Bennett DE, Camacho RJ, Otelea D, Kuritzkes DR, Fleury H, et al. (2009) Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS One 4: e4724.
-
(2009)
PLoS One
, vol.4
-
-
Bennett, D.E.1
Camacho, R.J.2
Otelea, D.3
Kuritzkes, D.R.4
Fleury, H.5
-
26
-
-
0030769354
-
Drug resistance during indinavir therapy is caused by mutations in the protease gene and in its Gag substrate cleavage sites
-
Zhang YM, Imamichi H, Imamichi T, Lane HC, Falloon J, et al. (1997) Drug resistance during indinavir therapy is caused by mutations in the protease gene and in its Gag substrate cleavage sites. J Virol 71: 6662-6670.
-
(1997)
J Virol
, vol.71
, pp. 6662-6670
-
-
Zhang, Y.M.1
Imamichi, H.2
Imamichi, T.3
Lane, H.C.4
Falloon, J.5
-
27
-
-
0036147360
-
Altered substrate specificity of drug-resistant human immunodeficiency virus type 1 protease
-
Dauber DS, Ziermann R, Parkin N, Maly DJ, Mahrus S, et al. (2002) Altered substrate specificity of drug-resistant human immunodeficiency virus type 1 protease. J Virol 76: 1359-1368.
-
(2002)
J Virol
, vol.76
, pp. 1359-1368
-
-
Dauber, D.S.1
Ziermann, R.2
Parkin, N.3
Maly, D.J.4
Mahrus, S.5
-
28
-
-
0035163687
-
Human immunodeficiency virus type 1 protease cleavage site mutations associated with protease inhibitor cross-resistance selected by indinavir, ritonavir, and/or saquinavir
-
Cote HC, Brumme ZL, Harrigan PR, (2001) Human immunodeficiency virus type 1 protease cleavage site mutations associated with protease inhibitor cross-resistance selected by indinavir, ritonavir, and/or saquinavir. J Virol 75: 589-594.
-
(2001)
J Virol
, vol.75
, pp. 589-594
-
-
Cote, H.C.1
Brumme, Z.L.2
Harrigan, P.R.3
-
29
-
-
20244387096
-
Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments
-
Wu TD, Schiffer CA, Gonzales MJ, Taylor J, Kantor R, et al. (2003) Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. J Virol 77: 4836-4847.
-
(2003)
J Virol
, vol.77
, pp. 4836-4847
-
-
Wu, T.D.1
Schiffer, C.A.2
Gonzales, M.J.3
Taylor, J.4
Kantor, R.5
-
30
-
-
32044456003
-
The backrub motion: how protein backbone shrugs when a sidechain dances
-
Davis IW, Arendall WBr, Richardson DC, Richardson JS, (2006) The backrub motion: how protein backbone shrugs when a sidechain dances. Structure 14: 265-274.
-
(2006)
Structure
, vol.14
, pp. 265-274
-
-
Davis, I.W.1
Arendall, W.B.2
Richardson, D.C.3
Richardson, J.S.4
-
31
-
-
0032573488
-
Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance
-
Huang H, Chopra R, Verdine GL, Harrison SC, (1998) Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 282: 1669-1675.
-
(1998)
Science
, vol.282
, pp. 1669-1675
-
-
Huang, H.1
Chopra, R.2
Verdine, G.L.3
Harrison, S.C.4
-
32
-
-
0030966369
-
Mutations within the primer grip region of HIV-1 reverse transcriptase result in loss of RNase H function
-
Palaniappan C, Wisniewski M, Jacques PS, Le Grice SF, Fay PJ, et al. (1997) Mutations within the primer grip region of HIV-1 reverse transcriptase result in loss of RNase H function. J Biol Chem 272: 11157-11164.
-
(1997)
J Biol Chem
, vol.272
, pp. 11157-11164
-
-
Palaniappan, C.1
Wisniewski, M.2
Jacques, P.S.3
Le Grice, S.F.4
Fay, P.J.5
-
33
-
-
0029893953
-
Role of the "helix clamp" in HIV-1 reverse transcriptase catalytic cycling as revealed by alanine-scanning mutagenesis
-
Beard WA, Minnick DT, Wade CL, Prasad R, Won RL, et al. (1996) Role of the "helix clamp" in HIV-1 reverse transcriptase catalytic cycling as revealed by alanine-scanning mutagenesis. J Biol Chem 271: 12213-12220.
-
(1996)
J Biol Chem
, vol.271
, pp. 12213-12220
-
-
Beard, W.A.1
Minnick, D.T.2
Wade, C.L.3
Prasad, R.4
Won, R.L.5
-
34
-
-
79551470095
-
Role of conformational sampling in computing mutation-induced changes in protein structure and stability
-
Kellogg EH, Leaver-Fay A, Baker D, (2011) Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins 79: 830-838.
-
(2011)
Proteins
, vol.79
, pp. 830-838
-
-
Kellogg, E.H.1
Leaver-Fay, A.2
Baker, D.3
-
35
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
-
Guerois R, Nielsen JE, Serrano L, (2002) Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 320: 369-387.
-
(2002)
J Mol Biol
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
36
-
-
34249777526
-
Eris: an automated estimator of protein stability
-
Yin S, Ding F, Dokholyan NV, (2007) Eris: an automated estimator of protein stability. Nat Methods 4: 466-467.
-
(2007)
Nat Methods
, vol.4
, pp. 466-467
-
-
Yin, S.1
Ding, F.2
Dokholyan, N.V.3
-
37
-
-
58149247893
-
Predicting free energy changes using structural ensembles
-
Benedix A, Becker CM, de Groot BL, Caflisch A, Bockmann RA, (2009) Predicting free energy changes using structural ensembles. Nat Methods 6: 3-4.
-
(2009)
Nat Methods
, vol.6
, pp. 3-4
-
-
Benedix, A.1
Becker, C.M.2
de Groot, B.L.3
Caflisch, A.4
Bockmann, R.A.5
-
38
-
-
84855998457
-
Global landscape of HIV-human protein complexes
-
Jager S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, et al. (2012) Global landscape of HIV-human protein complexes. Nature 481: 365-370.
-
(2012)
Nature
, vol.481
, pp. 365-370
-
-
Jager, S.1
Cimermancic, P.2
Gulbahce, N.3
Johnson, J.R.4
McGovern, K.E.5
-
40
-
-
70149090164
-
The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
-
Bakan A, Bahar I, (2009) The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc Natl Acad Sci U S A 106: 14349-14354.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 14349-14354
-
-
Bakan, A.1
Bahar, I.2
-
41
-
-
33746652529
-
Relation between native ensembles and experimental structures of proteins
-
Best RB, Lindorff-Larsen K, DePristo MA, Vendruscolo M, (2006) Relation between native ensembles and experimental structures of proteins. Proc Natl Acad Sci U S A 103: 10901-10906.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 10901-10906
-
-
Best, R.B.1
Lindorff-Larsen, K.2
DePristo, M.A.3
Vendruscolo, M.4
-
42
-
-
45649083705
-
A simple model of backbone flexibility improves modeling of side-chain conformational variability
-
Friedland GD, Linares AJ, Smith CA, Kortemme T, (2008) A simple model of backbone flexibility improves modeling of side-chain conformational variability. J Mol Biol 380: 757-774.
-
(2008)
J Mol Biol
, vol.380
, pp. 757-774
-
-
Friedland, G.D.1
Linares, A.J.2
Smith, C.A.3
Kortemme, T.4
-
43
-
-
74649086461
-
Structural bases for stability-function tradeoffs in antibiotic resistance
-
Thomas VL, McReynolds AC, Shoichet BK, (2010) Structural bases for stability-function tradeoffs in antibiotic resistance. J Mol Biol 396: 47-59.
-
(2010)
J Mol Biol
, vol.396
, pp. 47-59
-
-
Thomas, V.L.1
McReynolds, A.C.2
Shoichet, B.K.3
-
44
-
-
0036295508
-
Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs
-
Wang X, Minasov G, Shoichet BK, (2002) Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol 320: 85-95.
-
(2002)
J Mol Biol
, vol.320
, pp. 85-95
-
-
Wang, X.1
Minasov, G.2
Shoichet, B.K.3
-
46
-
-
0031849665
-
In vitro selection and characterization of human immunodeficiency virus type 1 variants with increased resistance to ABT-378, a novel protease inhibitor
-
Carrillo A, Stewart KD, Sham HL, Norbeck DW, Kohlbrenner WE, et al. (1998) In vitro selection and characterization of human immunodeficiency virus type 1 variants with increased resistance to ABT-378, a novel protease inhibitor. J Virol 72: 7532-7541.
-
(1998)
J Virol
, vol.72
, pp. 7532-7541
-
-
Carrillo, A.1
Stewart, K.D.2
Sham, H.L.3
Norbeck, D.W.4
Kohlbrenner, W.E.5
-
47
-
-
0034284897
-
Polymorphism of HIV type 1 gag p7/p1 and p1/p6 cleavage sites: clinical significance and implications for resistance to protease inhibitors
-
Bally F, Martinez R, Peters S, Sudre P, Telenti A, (2000) Polymorphism of HIV type 1 gag p7/p1 and p1/p6 cleavage sites: clinical significance and implications for resistance to protease inhibitors. AIDS Res Hum Retroviruses 16: 1209-1213.
-
(2000)
AIDS Res Hum Retroviruses
, vol.16
, pp. 1209-1213
-
-
Bally, F.1
Martinez, R.2
Peters, S.3
Sudre, P.4
Telenti, A.5
-
48
-
-
0032804864
-
Increased fitness of drug resistant HIV-1 protease as a result of acquisition of compensatory mutations during suboptimal therapy
-
Nijhuis M, Schuurman R, de Jong D, Erickson J, Gustchina E, et al. (1999) Increased fitness of drug resistant HIV-1 protease as a result of acquisition of compensatory mutations during suboptimal therapy. AIDS 13: 2349-2359.
-
(1999)
AIDS
, vol.13
, pp. 2349-2359
-
-
Nijhuis, M.1
Schuurman, R.2
de Jong, D.3
Erickson, J.4
Gustchina, E.5
-
50
-
-
0032562224
-
Domain flexibility in retroviral proteases: structural implications for drug resistant mutations
-
Rose RB, Craik CS, Stroud RM, (1998) Domain flexibility in retroviral proteases: structural implications for drug resistant mutations. Biochemistry 37: 2607-2621.
-
(1998)
Biochemistry
, vol.37
, pp. 2607-2621
-
-
Rose, R.B.1
Craik, C.S.2
Stroud, R.M.3
-
51
-
-
0028945211
-
Structural basis of drug resistance for the V82A mutant of HIV-1 proteinase
-
Baldwin ET, Bhat TN, Liu B, Pattabiraman N, Erickson JW, (1995) Structural basis of drug resistance for the V82A mutant of HIV-1 proteinase. Nat Struct Biol 2: 244-249.
-
(1995)
Nat Struct Biol
, vol.2
, pp. 244-249
-
-
Baldwin, E.T.1
Bhat, T.N.2
Liu, B.3
Pattabiraman, N.4
Erickson, J.W.5
-
52
-
-
0028014288
-
Characterization of human immunodeficiency virus type 1 variants with increased resistance to a C2-symmetric protease inhibitor
-
Ho DD, Toyoshima T, Mo H, Kempf DJ, Norbeck D, et al. (1994) Characterization of human immunodeficiency virus type 1 variants with increased resistance to a C2-symmetric protease inhibitor. J Virol 68: 2016-2020.
-
(1994)
J Virol
, vol.68
, pp. 2016-2020
-
-
Ho, D.D.1
Toyoshima, T.2
Mo, H.3
Kempf, D.J.4
Norbeck, D.5
-
53
-
-
0028286025
-
Selection of multiple human immunodeficiency virus type 1 variants that encode viral proteases with decreased sensitivity to an inhibitor of the viral protease
-
Kaplan AH, Michael SF, Wehbie RS, Knigge MF, Paul DA, et al. (1994) Selection of multiple human immunodeficiency virus type 1 variants that encode viral proteases with decreased sensitivity to an inhibitor of the viral protease. Proc Natl Acad Sci U S A 91: 5597-5601.
-
(1994)
Proc Natl Acad Sci U S A
, vol.91
, pp. 5597-5601
-
-
Kaplan, A.H.1
Michael, S.F.2
Wehbie, R.S.3
Knigge, M.F.4
Paul, D.A.5
-
54
-
-
1842454635
-
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
-
Perryman AL, Lin J-H, 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: 1108-1123.
-
(2004)
Protein Sci
, vol.13
, pp. 1108-1123
-
-
Perryman, A.L.1
Lin, J.-H.2
McCammon, J.A.3
-
55
-
-
61449101624
-
Predicting drug resistance of the HIV-1 protease using molecular interaction energy components
-
Hou T, Zhang W, Wang J, Wang W, (2009) Predicting drug resistance of the HIV-1 protease using molecular interaction energy components. Proteins 74: 837-846.
-
(2009)
Proteins
, vol.74
, pp. 837-846
-
-
Hou, T.1
Zhang, W.2
Wang, J.3
Wang, W.4
-
56
-
-
78651112937
-
A combined sequence-structure approach for predicting resistance to the non-nucleoside HIV-1 reverse transcriptase inhibitor Nevirapine
-
Ravich VL, Masso M, Vaisman II, (2011) A combined sequence-structure approach for predicting resistance to the non-nucleoside HIV-1 reverse transcriptase inhibitor Nevirapine. Biophys Chem 153: 168-172.
-
(2011)
Biophys Chem
, vol.153
, pp. 168-172
-
-
Ravich, V.L.1
Masso, M.2
Vaisman, I.I.3
-
57
-
-
33646036726
-
In vitro selection of mutations in human immunodeficiency virus type 1 reverse transcriptase that confer resistance to capravirine, a novel nonnucleoside reverse transcriptase inhibitor
-
Sato A, Hammond J, Alexander TN, Graham JP, Binford S, et al. (2006) In vitro selection of mutations in human immunodeficiency virus type 1 reverse transcriptase that confer resistance to capravirine, a novel nonnucleoside reverse transcriptase inhibitor. Antiviral Res 70: 66-74.
-
(2006)
Antiviral Res
, vol.70
, pp. 66-74
-
-
Sato, A.1
Hammond, J.2
Alexander, T.N.3
Graham, J.P.4
Binford, S.5
-
58
-
-
77956730468
-
Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains
-
Smith CA, Kortemme T, (2010) Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains. J Mol Biol 402: 460-474.
-
(2010)
J Mol Biol
, vol.402
, pp. 460-474
-
-
Smith, C.A.1
Kortemme, T.2
-
59
-
-
0037470581
-
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
-
Kortemme T, Morozov AV, Baker D, (2003) An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 326: 1239-1259.
-
(2003)
J Mol Biol
, vol.326
, pp. 1239-1259
-
-
Kortemme, T.1
Morozov, A.V.2
Baker, D.3
-
60
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis T, Karplus M, (1999) Effective energy function for proteins in solution. Proteins 35: 133-152.
-
(1999)
Proteins
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
61
-
-
1842326139
-
Bayesian statistical analysis of protein side-chain rotamer preferences
-
Dunbrack RL Jr, Cohen FE, (1997) Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 6: 1661-1681.
-
(1997)
Protein Sci
, vol.6
, pp. 1661-1681
-
-
Dunbrack Jr., R.L.1
Cohen, F.E.2
-
62
-
-
0034641749
-
Native protein sequences are close to optimal for their structures
-
Kuhlman B, Baker D, (2000) Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci U S A 97: 10383-10388.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 10383-10388
-
-
Kuhlman, B.1
Baker, D.2
-
63
-
-
33645891478
-
HIV-1 reverse transcriptase: a therapeutical target in the spotlight
-
Castro HC, Loureiro NI, Pujol-Luz M, Souza AM, Albuquerque MG, et al. (2006) HIV-1 reverse transcriptase: a therapeutical target in the spotlight. Curr Med Chem 13: 313-324.
-
(2006)
Curr Med Chem
, vol.13
, pp. 313-324
-
-
Castro, H.C.1
Loureiro, N.I.2
Pujol-Luz, M.3
Souza, A.M.4
Albuquerque, M.G.5
-
64
-
-
38049007454
-
Should we include connection domain mutations of HIV-1 reverse transcriptase in HIV resistance testing
-
Gotte M, (2007) Should we include connection domain mutations of HIV-1 reverse transcriptase in HIV resistance testing. PLoS Med 4: e346.
-
(2007)
PLoS Med
, vol.4
-
-
Gotte, M.1
-
65
-
-
35148845529
-
Characterization and structural analysis of novel mutations in human immunodeficiency virus type 1 reverse transcriptase involved in the regulation of resistance to nonnucleoside inhibitors
-
Ceccherini-Silberstein F, Svicher V, Sing T, Artese A, Santoro MM, et al. (2007) Characterization and structural analysis of novel mutations in human immunodeficiency virus type 1 reverse transcriptase involved in the regulation of resistance to nonnucleoside inhibitors. J Virol 81: 11507-11519.
-
(2007)
J Virol
, vol.81
, pp. 11507-11519
-
-
Ceccherini-Silberstein, F.1
Svicher, V.2
Sing, T.3
Artese, A.4
Santoro, M.M.5
-
66
-
-
0028947588
-
High resolution structures of HIV-1 RT from four RT-inhibitor complexes
-
Ren J, Esnouf R, Garman E, Somers D, Ross C, et al. (1995) High resolution structures of HIV-1 RT from four RT-inhibitor complexes. Nat Struct Biol 2: 293-302.
-
(1995)
Nat Struct Biol
, vol.2
, pp. 293-302
-
-
Ren, J.1
Esnouf, R.2
Garman, E.3
Somers, D.4
Ross, C.5
-
67
-
-
3242879168
-
Structural determinants and molecular mechanisms for the resistance of HIV-1 RT to nucleoside analogues
-
Deval J, Courcambeck J, Selmi B, Boretto J, Canard B, (2004) Structural determinants and molecular mechanisms for the resistance of HIV-1 RT to nucleoside analogues. Curr Drug Metab 5: 305-316.
-
(2004)
Curr Drug Metab
, vol.5
, pp. 305-316
-
-
Deval, J.1
Courcambeck, J.2
Selmi, B.3
Boretto, J.4
Canard, B.5
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