-
1
-
-
58149247893
-
Predicting free energy changes using structural ensembles
-
10.1038/nmeth0109-3 1:CAS:528:DC%2BD1cXhsFCku77K
-
Benedix A, Becker CM, de Groot BL, Caflisch A, Bockmann RA (2009) Predicting free energy changes using structural ensembles. Nat Methods 6(1):3-4
-
(2009)
Nat Methods
, vol.6
, Issue.1
, pp. 3-4
-
-
Benedix, A.1
Becker, C.M.2
De Groot, B.L.3
Caflisch, A.4
Bockmann, R.A.5
-
2
-
-
67650500988
-
CHARMM: The biomolecular simulation program
-
10.1002/jcc.21287 1:CAS:528:DC%2BD1MXms1Ciu70%3D
-
Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30(10):1545-614
-
(2009)
J Comput Chem
, vol.30
, Issue.10
, pp. 1545-614
-
-
Brooks, B.R.1
Brooks III, C.L.2
MacKerell Jr., A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, C.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
3
-
-
23144461249
-
I-Mutant2.0: Predicting stability changes upon mutation from the protein sequence or structure
-
Capriotti E, Fariselli P, Casadio R (2005) I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res 33(Web Server issue):W306-10
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.WEB SERVER ISSUE
-
-
Capriotti, E.1
Fariselli, P.2
Casadio, R.3
-
4
-
-
41949100049
-
Recent advances in implicit solvent-based methods for biomolecular simulations
-
10.1016/j.sbi.2008.01.003 1:CAS:528:DC%2BD1cXkvFCmu7Y%3D
-
Chen J, Brooks CL 3rd, Khandogin J (2008) Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol 18(2):140-8
-
(2008)
Curr Opin Struct Biol
, vol.18
, Issue.2
, pp. 140-8
-
-
Chen, J.1
Brooks III, C.L.2
Khandogin, J.3
-
6
-
-
0035490893
-
Isolation of methyl parathion-degrading strain M6 and cloning of the methyl parathion hydrolase gene
-
10.1128/AEM.67.10.4914-4918.2001 1:CAS:528:DC%2BD3MXns1Witbo%3D
-
Cui Z, Li S, Fu G (2001) Isolation of methyl parathion-degrading strain M6 and cloning of the methyl parathion hydrolase gene. Appl Environ Microbiol 67(10):4922-5
-
(2001)
Appl Environ Microbiol
, vol.67
, Issue.10
, pp. 4922-5
-
-
Cui, Z.1
Li, S.2
Fu, G.3
-
7
-
-
26244457622
-
Crystal structure of methyl parathion hydrolase from Pseudomonas sp. WBC-3
-
10.1016/j.jmb.2005.08.057 1:CAS:528:DC%2BD2MXhtVOktrvK
-
Dong Y, Bartlam M, Sun L, Zhou Y, Zhang Z, Zhang C, Rao Z, Zhang X (2005) Crystal structure of methyl parathion hydrolase from Pseudomonas sp. WBC-3. J Mol Biol 353(3):655-63
-
(2005)
J Mol Biol
, vol.353
, Issue.3
, pp. 655-63
-
-
Dong, Y.1
Bartlam, M.2
Sun, L.3
Zhou, Y.4
Zhang, Z.5
Zhang, C.6
Rao, Z.7
Zhang, X.8
-
8
-
-
23944462537
-
Statistics of protein library construction
-
10.1093/bioinformatics/bti516 1:CAS:528:DC%2BD2MXmt1eqsL4%3D
-
Firth AE, Patrick WM (2005) Statistics of protein library construction. Bioinformatics 21(15):3314-5
-
(2005)
Bioinformatics
, vol.21
, Issue.15
, pp. 3314-5
-
-
Firth, A.E.1
Patrick, W.M.2
-
9
-
-
62449293337
-
Rational stabilization of enzymes by computational redesign of surface charge-charge interactions
-
10.1073/pnas.0808220106 1:CAS:528:DC%2BD1MXislahs7Y%3D
-
Gribenko AV, Patel MM, Liu J, McCallum SA, Wang C, Makhatadze GI (2009) Rational stabilization of enzymes by computational redesign of surface charge-charge interactions. Proc Natl Acad Sci 106(8):2601-2606
-
(2009)
Proc Natl Acad Sci
, vol.106
, Issue.8
, pp. 2601-2606
-
-
Gribenko, A.V.1
Patel, M.M.2
Liu, J.3
McCallum, S.A.4
Wang, C.5
Makhatadze, G.I.6
-
10
-
-
73349137655
-
Enhancing thermostability of a Rhizomucor miehei lipase by engineering a disulfide bond and displaying on the yeast cell surface
-
10.1007/s00253-009-2067-8 1:CAS:528:DC%2BD1MXht12ms7nN
-
Han ZL, Han SY, Zheng SP, Lin Y (2009) Enhancing thermostability of a Rhizomucor miehei lipase by engineering a disulfide bond and displaying on the yeast cell surface. Appl Microbiol Biotechnol 85(1):117-26
-
(2009)
Appl Microbiol Biotechnol
, vol.85
, Issue.1
, pp. 117-26
-
-
Han, Z.L.1
Han, S.Y.2
Zheng, S.P.3
Lin, Y.4
-
11
-
-
65249175725
-
A family of thermostable fungal cellulases created by structure-guided recombination
-
10.1073/pnas.0901417106 1:CAS:528:DC%2BD1MXkvFGhtbs%3D
-
Heinzelman P, Snow CD, Wu I, Nguyen C, Villalobos A, Govindarajan S, Minshull J, Arnold FH (2009) A family of thermostable fungal cellulases created by structure-guided recombination. Proc Natl Acad Sci U S A 106(14):5610-5
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, Issue.14
, pp. 5610-5
-
-
Heinzelman, P.1
Snow, C.D.2
Wu, I.3
Nguyen, C.4
Villalobos, A.5
Govindarajan, S.6
Minshull, J.7
Arnold, F.H.8
-
12
-
-
33846219593
-
Engineering a de novo internal disulfide bridge to improve the thermal stability of xylanase from Bacillus stearothermophilus No. 236
-
10.1016/j.jbiotec.2006.07.005 1:CAS:528:DC%2BD28Xht1ShtL3F
-
Jeong MY, Kim S, Yun CW, Choi YJ, Cho SG (2007) Engineering a de novo internal disulfide bridge to improve the thermal stability of xylanase from Bacillus stearothermophilus No. 236. J Biotechnol 127(2):300-9
-
(2007)
J Biotechnol
, vol.127
, Issue.2
, pp. 300-9
-
-
Jeong, M.Y.1
Kim, S.2
Yun, C.W.3
Choi, Y.J.4
Cho, S.G.5
-
13
-
-
61849134386
-
Robust prediction of mutation-induced protein stability change by property encoding of amino acids
-
10.1093/protein/gzn063 1:CAS:528:DC%2BD1MXjsFGqt7k%3D
-
Kang S, Chen G, Xiao G (2009) Robust prediction of mutation-induced protein stability change by property encoding of amino acids. Protein Eng Des Sel 22(2):75-83
-
(2009)
Protein Eng des Sel
, vol.22
, Issue.2
, pp. 75-83
-
-
Kang, S.1
Chen, G.2
Xiao, G.3
-
14
-
-
77952706843
-
Performance of protein stability predictors
-
10.1002/humu.21242 1:CAS:528:DC%2BC3cXosl2lu70%3D
-
Khan S, Vihinen M (2010) Performance of protein stability predictors. Hum Mutat 31(6):675-84
-
(2010)
Hum Mutat
, vol.31
, Issue.6
, pp. 675-84
-
-
Khan, S.1
Vihinen, M.2
-
15
-
-
18244373419
-
Computational thermostabilization of an enzyme
-
10.1126/science.1107387 1:CAS:528:DC%2BD2MXjvVant7s%3D
-
Korkegian A, Black ME, Baker D, Stoddard BL (2005) Computational thermostabilization of an enzyme. Science 308(5723):857-60
-
(2005)
Science
, vol.308
, Issue.5723
, pp. 857-60
-
-
Korkegian, A.1
Black, M.E.2
Baker, D.3
Stoddard, B.L.4
-
16
-
-
34547748376
-
Implication for buried polar contacts and ion pairs in hyperthermostable enzymes
-
10.1111/j.1742-4658.2007.05956.x 1:CAS:528:DC%2BD2sXhtVSmt7rO
-
Matsui I, Harata K (2007) Implication for buried polar contacts and ion pairs in hyperthermostable enzymes. FEBS J 274(16):4012-22
-
(2007)
FEBS J
, vol.274
, Issue.16
, pp. 4012-22
-
-
Matsui, I.1
Harata, K.2
-
18
-
-
24044554219
-
Site-saturation mutagenesis is more efficient than DNA shuffling for the directed evolution of β-fucosidase from β-galactosidase
-
10.1016/j.jmb.2005.07.020 1:CAS:528:DC%2BD2MXpslyltbc%3D
-
Parikh MR, Matsumura I (2005) Site-saturation mutagenesis is more efficient than DNA shuffling for the directed evolution of β-fucosidase from β-galactosidase. J Mol Biol 352(3):621-628
-
(2005)
J Mol Biol
, vol.352
, Issue.3
, pp. 621-628
-
-
Parikh, M.R.1
Matsumura, I.2
-
19
-
-
23944525846
-
Strategies and computational tools for improving randomized protein libraries
-
10.1016/j.bioeng.2005.06.001 1:CAS:528:DC%2BD2MXpsVWmu74%3D
-
Patrick WM, Firth AE (2005) Strategies and computational tools for improving randomized protein libraries. Biomol Eng 22(4):105-12
-
(2005)
Biomol Eng
, vol.22
, Issue.4
, pp. 105-12
-
-
Patrick, W.M.1
Firth, A.E.2
-
20
-
-
0041765676
-
User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries
-
10.1093/protein/gzg057 1:CAS:528:DC%2BD3sXlsl2ktLk%3D
-
Patrick WM, Firth AE, Blackburn JM (2003) User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries. Protein Eng 16(6):451-7
-
(2003)
Protein Eng
, vol.16
, Issue.6
, pp. 451-7
-
-
Patrick, W.M.1
Firth, A.E.2
Blackburn, J.M.3
-
21
-
-
79952487469
-
Protein rigidity and thermophilic adaptation
-
10.1002/prot.22946 1:CAS:528:DC%2BC3MXkvVWrsLk%3D
-
Radestock S, Gohlke H (2011) Protein rigidity and thermophilic adaptation. Proteins 79(4):1089-108
-
(2011)
Proteins
, vol.79
, Issue.4
, pp. 1089-108
-
-
Radestock, S.1
Gohlke, H.2
-
22
-
-
34248567845
-
Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes
-
10.1038/nprot.2007.72 1:CAS:528:DC%2BD2sXhtFGnur%2FP
-
Reetz MT, Carballeira JD (2007) Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat Protoc 2(4):891-903
-
(2007)
Nat Protoc
, vol.2
, Issue.4
, pp. 891-903
-
-
Reetz, M.T.1
Carballeira, J.D.2
-
23
-
-
33845288649
-
Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability
-
10.1002/anie.200602795 1:CAS:528:DC%2BD28Xht12rs7zM
-
Reetz MT, Carballeira JD, Vogel A (2006) Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angew Chem Int Ed Engl 45(46):7745-51
-
(2006)
Angew Chem Int Ed Engl
, vol.45
, Issue.46
, pp. 7745-51
-
-
Reetz, M.T.1
Carballeira, J.D.2
Vogel, A.3
-
24
-
-
77954274719
-
Iterative saturation mutagenesis accelerates laboratory evolution of enzyme stereoselectivity: Rigorous comparison with traditional methods
-
10.1021/ja1030479 1:CAS:528:DC%2BC3cXntF2jsbk%3D
-
Reetz MT, Prasad S, Carballeira JD, Gumulya Y, Bocola M (2010) Iterative saturation mutagenesis accelerates laboratory evolution of enzyme stereoselectivity: rigorous comparison with traditional methods. J Am Chem Soc 132(26):9144-52
-
(2010)
J Am Chem Soc
, vol.132
, Issue.26
, pp. 9144-52
-
-
Reetz, M.T.1
Prasad, S.2
Carballeira, J.D.3
Gumulya, Y.4
Bocola, M.5
-
26
-
-
23144436398
-
FoldX web server: An online force field
-
Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L (2005) The FoldX web server: an online force field. Nucleic Acids Res 33 (Web Server issue):W382-8
-
Nucleic Acids Res
, vol.33
, Issue.WEB SERVER ISSUE
-
-
Schymkowitz, J.1
Borg, J.2
Stricher, F.3
Nys, R.4
Rousseau, F.5
Serrano, L.6
-
27
-
-
61449128254
-
Error-prone PCR of a fungal xylanase for improvement of its alkaline and thermal stability
-
10.1111/j.1574-6968.2009.01519.x 1:CAS:528:DC%2BD1MXjsVajtr4%3D
-
Stephens DE, Singh S, Permaul K (2009) Error-prone PCR of a fungal xylanase for improvement of its alkaline and thermal stability. FEMS Microbiol Lett 293(1):42-7
-
(2009)
FEMS Microbiol Lett
, vol.293
, Issue.1
, pp. 42-7
-
-
Stephens, D.E.1
Singh, S.2
Permaul, K.3
-
28
-
-
75549091169
-
Rational engineering of cytochromes P450 2B6 and 2B11 for enhanced stability: Insights into structural importance of residue 334
-
10.1016/j.abb.2009.11.026 1:CAS:528:DC%2BC3cXhtlCnsLg%3D
-
Talakad JC, Wilderman PR, Davydov DR, Kumar S, Halpert JR (2010) Rational engineering of cytochromes P450 2B6 and 2B11 for enhanced stability: insights into structural importance of residue 334. Arch Biochem Biophys 494(2):151-158
-
(2010)
Arch Biochem Biophys
, vol.494
, Issue.2
, pp. 151-158
-
-
Talakad, J.C.1
Wilderman, P.R.2
Davydov, D.R.3
Kumar, S.4
Halpert, J.R.5
-
29
-
-
38649091045
-
Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines
-
10.1186/1471-2105-8-450
-
Tian J, Wu N, Guo X, Guo J, Zhang J, Fan Y (2007) Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines. BMC Bioinforma 8:450
-
(2007)
BMC Bioinforma
, vol.8
, pp. 450
-
-
Tian, J.1
Wu, N.2
Guo, X.3
Guo, J.4
Zhang, J.5
Fan, Y.6
-
30
-
-
78449306754
-
Enhanced thermostability of methyl parathion hydrolase from Ochrobactrum sp. M231 by rationally engineering a glycine to proline mutation
-
10.1111/j.1742-4658.2010.07895.x 1:CAS:528:DC%2BC3cXhsFKmsrnP
-
Tian J, Wang P, Gao S, Chu X, Wu N, Fan Y (2010a) Enhanced thermostability of methyl parathion hydrolase from Ochrobactrum sp. M231 by rationally engineering a glycine to proline mutation. FEBS J 277:4901-4908
-
(2010)
FEBS J
, vol.277
, pp. 4901-4908
-
-
Tian, J.1
Wang, P.2
Gao, S.3
Chu, X.4
Wu, N.5
Fan, Y.6
-
31
-
-
77954062293
-
Predicting changes in protein thermostability brought about by single- or multi-site mutations
-
10.1186/1471-2105-11-370
-
Tian J, Wu N, Chu X, Fan Y (2010b) Predicting changes in protein thermostability brought about by single- or multi-site mutations. BMC Bioinforma 11:370
-
(2010)
BMC Bioinforma
, vol.11
, pp. 370
-
-
Tian, J.1
Wu, N.2
Chu, X.3
Fan, Y.4
-
32
-
-
0035098779
-
Hyperthermophilic enzymes: Sources, uses, and molecular mechanisms for thermostability
-
10.1128/MMBR.65.1.1-43.2001 1:CAS:528:DC%2BD3MXisFyms74%3D
-
Vieille C, Zeikus GJ (2001) Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 65(1):1-43
-
(2001)
Microbiol Mol Biol Rev
, vol.65
, Issue.1
, pp. 1-43
-
-
Vieille, C.1
Zeikus, G.J.2
-
33
-
-
77955801822
-
Cloning of a Methyl Parathion Hydrolase Gene from Ochrobactrum sp
-
In Chinese
-
Xiao W, Chu X, Tian J, Guo J, Wu N (2008) Cloning of a Methyl Parathion Hydrolase Gene from Ochrobactrum sp. Journal of Agricultural Science and Technology (In Chinese)(S1):99-102
-
(2008)
Journal of Agricultural Science and Technology
, Issue.S1
, pp. 99-102
-
-
Xiao, W.1
Chu, X.2
Tian, J.3
Guo, J.4
Wu, N.5
-
34
-
-
33750804116
-
Cloning of mpd gene from a chlorpyrifos-degrading bacterium and use of this strain in bioremediation of contaminated soil
-
10.1111/j.1574-6968.2006.00478.x 1:CAS:528:DC%2BD28XhtlSmur7M
-
Yang C, Liu N, Guo X, Qiao C (2006) Cloning of mpd gene from a chlorpyrifos-degrading bacterium and use of this strain in bioremediation of contaminated soil. FEMS Microbiol Lett 265(1):118-25
-
(2006)
FEMS Microbiol Lett
, vol.265
, Issue.1
, pp. 118-25
-
-
Yang, C.1
Liu, N.2
Guo, X.3
Qiao, C.4
-
35
-
-
75249104215
-
Cotranslocation of methyl parathion hydrolase to the periplasm and of organophosphorus hydrolase to the cell surface of Escherichia coli by the Tat pathway and ice nucleation protein display system
-
10.1128/AEM.02162-09 1:CAS:528:DC%2BC3cXksVCitrY%3D
-
Yang C, Freudl R, Qiao C, Mulchandani A (2010) Cotranslocation of methyl parathion hydrolase to the periplasm and of organophosphorus hydrolase to the cell surface of Escherichia coli by the Tat pathway and ice nucleation protein display system. Appl Environ Microbiol 76(2):434-40
-
(2010)
Appl Environ Microbiol
, vol.76
, Issue.2
, pp. 434-40
-
-
Yang, C.1
Freudl, R.2
Qiao, C.3
Mulchandani, A.4
-
36
-
-
34249777526
-
Eris: An automated estimator of protein stability
-
10.1038/nmeth0607-466 1:CAS:528:DC%2BD2sXlvVykurg%3D
-
Yin S, Ding F, Dokholyan NV (2007) Eris: an automated estimator of protein stability. Nat Methods 4(6):466-7
-
(2007)
Nat Methods
, vol.4
, Issue.6
, pp. 466-7
-
-
Yin, S.1
Ding, F.2
Dokholyan, N.V.3
-
37
-
-
71449110779
-
Expression of methyl parathion hydrolase in Pichia pastoris
-
10.1007/s00284-009-9484-x 1:CAS:528:DC%2BD1MXhsValurnO
-
Yu H, Yan X, Shen W, Hong Q, Zhang J, Shen Y, Li S (2009) Expression of methyl parathion hydrolase in Pichia pastoris. Curr Microbiol 59(6):573-8
-
(2009)
Curr Microbiol
, vol.59
, Issue.6
, pp. 573-8
-
-
Yu, H.1
Yan, X.2
Shen, W.3
Hong, Q.4
Zhang, J.5
Shen, Y.6
Li, S.7
|