-
1
-
-
0029000550
-
Expression and purification of a recombinant tobacco etch virus NIa proteinase: Biochemical analyses of the full-length and a naturally occur- ring truncated proteinase form
-
10.1006/viro.1995.1331 1:CAS:528:DyaK2MXmsVahu70%3D
-
Parks TD, Howard ED, Wolpert TJ, Arp DJ, Dougherty WG (1995) Expression and purification of a recombinant tobacco etch virus NIa proteinase: biochemical analyses of the full-length and a naturally occur- ring truncated proteinase form. Virology 210:194-201
-
(1995)
Virology
, vol.210
, pp. 194-201
-
-
Parks, T.D.1
Howard, E.D.2
Wolpert, T.J.3
Arp, D.J.4
Dougherty, W.G.5
-
2
-
-
0033939135
-
Controlled intracellular processing of fusion proteins by TEV protease
-
10.1006/prep.2000.1251 1:CAS:528:DC%2BD3cXkt1Knt70%3D
-
Kapust RB, Waugh DS (2000) Controlled intracellular processing of fusion proteins by TEV protease. Protein Expr Purif 19:312-318
-
(2000)
Protein Expr Purif
, vol.19
, pp. 312-318
-
-
Kapust, R.B.1
Waugh, D.S.2
-
3
-
-
15244363693
-
Self-cleavage of fusion protein in vivo using TEV protease to yield native protein
-
10.1110/ps.041129605 1:CAS:528:DC%2BD2MXislOnu78%3D
-
Shih YP, Wu HC, Hu SM, Wang TF, Wang AHJ (2005) Self-cleavage of fusion protein in vivo using TEV protease to yield native protein. Protein Sci 14:936-941
-
(2005)
Protein Sci
, vol.14
, pp. 936-941
-
-
Shih, Y.P.1
Wu, H.C.2
Hu, S.M.3
Wang, T.F.4
Wang, A.H.J.5
-
4
-
-
78649652504
-
TEV protease-facilitated stoichiometric delivery of multiple genes using a single expression vector
-
10.1002/pro.518 1:CAS:528:DC%2BC3cXhsFCntbbN
-
Chen X, Pham E, Truong K (2010) TEV protease-facilitated stoichiometric delivery of multiple genes using a single expression vector. Protein Sci 19:2379-2388
-
(2010)
Protein Sci
, vol.19
, pp. 2379-2388
-
-
Chen, X.1
Pham, E.2
Truong, K.3
-
5
-
-
80054052318
-
An overview of enzymatic reagents for the removal of affinity tags
-
10.1016/j.pep.2011.08.005 1:CAS:528:DC%2BC3MXhtlejtLvL
-
Waugh DS (2011) An overview of enzymatic reagents for the removal of affinity tags. Protein Expr Purif 80:283-293
-
(2011)
Protein Expr Purif
, vol.80
, pp. 283-293
-
-
Waugh, D.S.1
-
6
-
-
84859914061
-
In vivo and in vitro characterization of TEV protease mutants
-
10.1016/j.pep.2012.03.011 1:CAS:528:DC%2BC38Xns1Cgs7c%3D
-
Wei L, Cai X, Qi Z, Rong L, Cheng B, Fan J (2012) In vivo and in vitro characterization of TEV protease mutants. Protein Expr Purif 83:157-163
-
(2012)
Protein Expr Purif
, vol.83
, pp. 157-163
-
-
Wei, L.1
Cai, X.2
Qi, Z.3
Rong, L.4
Cheng, B.5
Fan, J.6
-
7
-
-
0035711194
-
Tobacco etch virus protease: Mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency
-
10.1093/protein/14.12.993 1:CAS:528:DC%2BD38XhsFOgtb0%3D
-
Kapust RB, Tözsér J, Fox JD, Anderson DE, Cherry S, Copeland TD, Waugh DS (2001) Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. Protein Eng 14:993-1000
-
(2001)
Protein Eng
, vol.14
, pp. 993-1000
-
-
Kapust, R.B.1
Tözsér, J.2
Fox, J.D.3
Anderson, D.E.4
Cherry, S.5
Copeland, T.D.6
Waugh, D.S.7
-
8
-
-
30944459888
-
Improved solubility of TEV protease by directed evolution
-
10.1016/j.jbiotec.2005.08.006
-
Van den Berg S, Löfdahl PA, Härd T, Berglund H (2006) Improved solubility of TEV protease by directed evolution. J Biotechnol 121:291-298
-
(2006)
J Biotechnol
, vol.121
, pp. 291-298
-
-
Van Den Berg, S.1
Löfdahl, P.A.2
Härd, T.3
Berglund, H.4
-
9
-
-
35648952843
-
Enhancing the stability and solubility of TEV protease using in silico design
-
10.1110/ps.072822507 1:CAS:528:DC%2BD2sXht1ygu7jM
-
Cabrita LD, Gilis D, Robertson AL, Dehouck Y, Rooman M, Bottomley SP (2007) Enhancing the stability and solubility of TEV protease using in silico design. Protein Sci 16:2360-2367
-
(2007)
Protein Sci
, vol.16
, pp. 2360-2367
-
-
Cabrita, L.D.1
Gilis, D.2
Robertson, A.L.3
Dehouck, Y.4
Rooman, M.5
Bottomley, S.P.6
-
10
-
-
0037184981
-
Structural basis for the substrate specificity of tobacco etch virus protease
-
10.1074/jbc.M207224200 1:CAS:528:DC%2BD38Xps12ntr4%3D
-
Phan J, Zdanov A, Evdokimov AG, Tropea JE, Peters HK III, Kapust RB, Li M, Wlodawer A, Waugh DS (2002) Structural basis for the substrate specificity of tobacco etch virus protease. J Biol Chem 277:50564-50572
-
(2002)
J Biol Chem
, vol.277
, pp. 50564-50572
-
-
Phan, J.1
Zdanov, A.2
Evdokimov, A.G.3
Tropea, J.E.4
Peters III, H.K.5
Kapust, R.B.6
Li, M.7
Wlodawer, A.8
Waugh, D.S.9
-
11
-
-
20444374108
-
Crystal structure of tobacco etch virus protease shows the protein C terminus bound within the active site
-
10.1016/j.jmb.2005.04.013 1:CAS:528:DC%2BD2MXltVejt78%3D
-
Nunn CM, Jeeves M, Cliff MJ, Urquhart GT, George RR, Chao LH, Tscuchia Y, Djordjevic S (2005) Crystal structure of tobacco etch virus protease shows the protein C terminus bound within the active site. J Mol Biol 350:145-155
-
(2005)
J Mol Biol
, vol.350
, pp. 145-155
-
-
Nunn, C.M.1
Jeeves, M.2
Cliff, M.J.3
Urquhart, G.T.4
George, R.R.5
Chao, L.H.6
Tscuchia, Y.7
Djordjevic, S.8
-
12
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
10.1038/nsb0902-646 1:CAS:528:DC%2BD38Xms1ajt7o%3D
-
Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9:646-652
-
(2002)
Nat Struct Biol
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
13
-
-
34249930159
-
Single-molecule experiments in vitro and in silico
-
10.1126/science.1137591 1:CAS:528:DC%2BD2sXls1Kit7g%3D
-
Sotomayor M, Schulten K (2007) Single-molecule experiments in vitro and in silico. Science 316:1144-1148
-
(2007)
Science
, vol.316
, pp. 1144-1148
-
-
Sotomayor, M.1
Schulten, K.2
-
14
-
-
79551472252
-
Structural insights into a low-spin myoglobin variant with bis-histidine coordination from molecular modeling
-
10.1002/prot.22928 1:CAS:528:DC%2BC3MXjtFahsLg%3D
-
Lin YW (2011) Structural insights into a low-spin myoglobin variant with bis-histidine coordination from molecular modeling. Proteins 79:679-684
-
(2011)
Proteins
, vol.79
, pp. 679-684
-
-
Lin, Y.W.1
-
15
-
-
84861234047
-
Molecular modeling of cytochrome b5 with a single cytochrome c-like thioether linkage
-
10.1007/s00894-011-1189-y 1:CAS:528:DC%2BC38XkvVeksbg%3D
-
Lin YW, Wu YM, Liao LF, Nie CM (2012) Molecular modeling of cytochrome b5 with a single cytochrome c-like thioether linkage. J Mol Model 18:1553-1560
-
(2012)
J Mol Model
, vol.18
, pp. 1553-1560
-
-
Lin, Y.W.1
Wu, Y.M.2
Liao, L.F.3
Nie, C.M.4
-
16
-
-
77954584856
-
Thrombin allosteric modulation revisited: A molecular dynamics study
-
10.1007/s00894-009-0590-2
-
Amorim HLN, Netz PA, Guimarães JA (2010) Thrombin allosteric modulation revisited: a molecular dynamics study. J Mol Model 16:725-735
-
(2010)
J Mol Model
, vol.16
, pp. 725-735
-
-
Amorim, H.L.N.1
Netz, P.A.2
Guimarães, J.A.3
-
17
-
-
0027136282
-
Comparative protein modeling by satisfaction of spatial restraints
-
10.1006/jmbi.1993.1626 1:CAS:528:DyaK2cXnt1ylug%3D%3D
-
Sali A, Blundell TL (1993) Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 234:779-815
-
(1993)
J Mol Biol
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
18
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
10.1146/annurev.biophys.29.1.291
-
MartI-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A (2000) Comparative protein structure modeling of genes and genomes. Biophys Biomol Struct Rev 29:291-325
-
(2000)
Biophys Biomol Struct Rev
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.C.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
19
-
-
0033810049
-
Modeling of loops in protein structures
-
10.1110/ps.9.9.1753 1:CAS:528:DC%2BD3cXntFamsL8%3D
-
Fiser A, Do RK, Sali A (2000) Modeling of loops in protein structures. Protein Sci 9:1753-1773
-
(2000)
Protein Sci
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.K.2
Sali, A.3
-
20
-
-
49649114605
-
Protein structure modeling with MODELLER
-
10.1007/978-1-60327-058-8-8 1:CAS:528:DC%2BD1cXktlKqsrg%3D
-
Eswar N, Eramian D, Webb B, Shen MY, Sali A (2008) Protein structure modeling with MODELLER. Methods Mol Biol 426:145-159
-
(2008)
Methods Mol Biol
, vol.426
, pp. 145-159
-
-
Eswar, N.1
Eramian, D.2
Webb, B.3
Shen, M.Y.4
Sali, A.5
-
21
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
10.1002/jcc.20289 1:CAS:528:DC%2BD2MXht1SlsbbJ
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781-1802
-
(2005)
J Comput Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
22
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
10.1021/jp973084f 1:CAS:528:DyaK1cXivVOlsb4%3D
-
MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlen-krich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M et al (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlen-Krich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
23
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
10.1063/1.445869 1:CAS:528:DyaL3sXksF2htL4%3D
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
24
-
-
0035449971
-
Optimized particle-mesh ewald/multiple-time step integration for molecular dynamics simulations
-
10.1063/1.1389854 1:CAS:528:DC%2BD3MXmt1ajsr8%3D
-
Batcho PF, Case DA, Schlick T (2001) Optimized particle-mesh ewald/multiple-time step integration for molecular dynamics simulations. J Chem Phys 115:4003-4018
-
(2001)
J Chem Phys
, vol.115
, pp. 4003-4018
-
-
Batcho, P.F.1
Case, D.A.2
Schlick, T.3
-
25
-
-
33645961739
-
A smooth particle mesh Ewald method
-
10.1063/1.470117 1:CAS:528:DyaK2MXptlehtrw%3D
-
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577-8593
-
(1995)
J Chem Phys
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
26
-
-
84986440341
-
SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
-
10.1002/jcc.540130805 1:CAS:528:DyaK38Xlslykt7o%3D
-
Miyamoto S, Kollman PA (1992) SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem 13:952-962
-
(1992)
J Comput Chem
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
27
-
-
48749148224
-
RATTLE: A velocity version of the SHAKE algorithm for molecular dynamics calculations
-
10.1016/0021-9991(83)90014-1 1:CAS:528:DyaL2cXjvFOntw%3D%3D
-
Andersen HC (1983) RATTLE: a velocity version of the SHAKE algorithm for molecular dynamics calculations. J Comput Phys 52:24-34
-
(1983)
J Comput Phys
, vol.52
, pp. 24-34
-
-
Andersen, H.C.1
-
28
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
10.1063/1.448118 1:CAS:528:DyaL2cXmtlGksbY%3D
-
Berendsen HJC, Postma JPM, Van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-3690
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
29
-
-
36449003554
-
Constant-pressure molecular dynamics algorithms
-
10.1063/1.467468 1:CAS:528:DyaK2cXmtFeht7o%3D
-
Martyna GJ, Tobias DJ, Klein ML (1994) Constant-pressure molecular dynamics algorithms. J Chem Phys 101:4177-4189
-
(1994)
J Chem Phys
, vol.101
, pp. 4177-4189
-
-
Martyna, G.J.1
Tobias, D.J.2
Klein, M.L.3
-
30
-
-
0029878720
-
VMD: Visual molecular dynamics
-
10.1016/0263-7855(96)00018-5 1:CAS:528:DyaK28Xis12nsrg%3D
-
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33-38
-
(1996)
J Mol Graph
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
31
-
-
0029619259
-
Knowledge-based secondary structure assignment
-
10.1002/prot.340230412 1:CAS:528:DyaK28Xht1yluw%3D%3D
-
Frishman D, Argos P (1995) Knowledge-based secondary structure assignment. Proteins 23:566-579
-
(1995)
Proteins
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
32
-
-
79955690859
-
Structural and thermodynamic investigations on the aggregation and folding of acylphosphatase by molecular dynamics simulations and solvation free energy analysis
-
10.1021/ja1116233 1:CAS:528:DC%2BC3MXkvVCltL8%3D
-
Chong SH, Lee C, Kang G, ParK M, Ham S (2011) Structural and thermodynamic investigations on the aggregation and folding of acylphosphatase by molecular dynamics simulations and solvation free energy analysis. J Am Chem Soc 133:7075-7083
-
(2011)
J Am Chem Soc
, vol.133
, pp. 7075-7083
-
-
Chong, S.H.1
Lee, C.2
Kang, G.3
Park, M.4
Ham, S.5
-
33
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
10.1016/0022-2836(71)90324-X 1:CAS:528:DyaE3MXht1Shtrk%3D
-
Lee B, Richards FM (1971) The interpretation of protein structures: estimation of static accessibility. J Mol Biol 55:379-400
-
(1971)
J Mol Biol
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
34
-
-
83655169803
-
Influence of the pathogenic mutations T188K/R/A on the structural stability and misfolding of human prion protein: Insight from the molecular dynamics simulations
-
10.1016/j.bbagen.2011.11.013 1:CAS:528:DC%2BC38Xos1ygsQ%3D%3D
-
Guo J, Ning L, Ren H, Liu H, Yao X (2012) Influence of the pathogenic mutations T188K/R/A on the structural stability and misfolding of human prion protein: insight from the molecular dynamics simulations. Biochim Biophys Acta 1820:116-123
-
(2012)
Biochim Biophys Acta
, vol.1820
, pp. 116-123
-
-
Guo, J.1
Ning, L.2
Ren, H.3
Liu, H.4
Yao, X.5
-
35
-
-
84857568783
-
Mechanisms of loss of functions of human angiogenin variants implicated in amyotrophic lateral sclerosis
-
10.1371/journal.pone.0032479 1:CAS:528:DC%2BC38XjsFyktrk%3D
-
Padhi AK, Kumar H, Vasaikar SV, Jayaram B, Gomes J (2012) Mechanisms of loss of functions of human angiogenin variants implicated in amyotrophic lateral sclerosis. PLoS One 7(2):e32479
-
(2012)
PLoS One
, vol.7
, Issue.2
, pp. 32479
-
-
Padhi, A.K.1
Kumar, H.2
Vasaikar, S.V.3
Jayaram, B.4
Gomes, J.5
-
36
-
-
84864660051
-
Understanding the basis of drug resistance of the mutants of αβ-Tubulin dimer via molecular dynamics simulations
-
10.1371/journal.pone.0042351 1:CAS:528:DC%2BC38XhtFyru7%2FP
-
Natarajan K, Senapati S (2012) Understanding the basis of drug resistance of the mutants of αβ-Tubulin dimer via molecular dynamics simulations. PLoS One 7(8):e42351
-
(2012)
PLoS One
, vol.7
, Issue.8
, pp. 42351
-
-
Natarajan, K.1
Senapati, S.2
-
37
-
-
64849101493
-
Protein dynamism and evolvability
-
10.1126/science.1169375 1:CAS:528:DC%2BD1MXktFalsL8%3D
-
Tokuriki N, Tawfik DS (2009) Protein dynamism and evolvability. Science 324:203-207
-
(2009)
Science
, vol.324
, pp. 203-207
-
-
Tokuriki, N.1
Tawfik, D.S.2
|