메뉴 건너뛰기




Volumn 1179, Issue , 2014, Pages 315-333

Computational tools for directed evolution: A comparison of prospective and retrospective strategies

Author keywords

ASRA; Computational tools; Directed evolution; Library generation; Mutant; OPTCOMB; ProSAR; Protein; SCHEMA; Scoring

Indexed keywords

AMINO ACID SEQUENCE; COMBINATORIAL LIBRARY; DIRECTED MOLECULAR EVOLUTION; ENANTIOSELECTIVITY; GENE LIBRARY; GENE SEQUENCE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HYDROPHOBICITY; MOLECULAR LIBRARY; MUTANT; MUTATION; NONHUMAN; PRIORITY JOURNAL; PROSPECTIVE STUDY; PROTEIN ENGINEERING; PROTEIN STRUCTURE; RETROSPECTIVE STUDY; REVIEW; SCORING SYSTEM; SEQUENCE ALIGNMENT; BIOLOGY; PROCEDURES;

EID: 84925883593     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1053-3_21     Document Type: Review
Times cited : (13)

References (48)
  • 1
    • 36749020130 scopus 로고    scopus 로고
    • Protein engineers turned evolutionists
    • Peisajovich SG, Tawfik DS (2007) Protein engineers turned evolutionists. Nat Methods 4(12):991-994
    • (2007) Nat Methods , vol.4 , Issue.12 , pp. 991-994
    • Peisajovich, S.G.1    Tawfik, D.S.2
  • 3
    • 24644518006 scopus 로고    scopus 로고
    • Design of combinatorial protein libraries of optimal size
    • Saraf MC, Gupta A, Maranas CD (2005) Design of combinatorial protein libraries of optimal size. Proteins 60(4):769-777
    • (2005) Proteins , vol.60 , Issue.4 , pp. 769-777
    • Saraf, M.C.1    Gupta, A.2    Maranas, C.D.3
  • 4
    • 34548803632 scopus 로고    scopus 로고
    • Optimal protein library design using recombination or point mutations based on sequence-based scoring functions
    • Pantazes RJ, Saraf MC, Maranas CD (2007) Optimal protein library design using recombination or point mutations based on sequence-based scoring functions. Protein Eng Des Sel 20(8):361-373
    • (2007) Protein Eng des Sel , vol.20 , Issue.8 , pp. 361-373
    • Pantazes, R.J.1    Saraf, M.C.2    Maranas, C.D.3
  • 5
    • 84859882358 scopus 로고    scopus 로고
    • Enhancing the efficiency of directed evolution in focused enzyme libraries by the adaptive substituent reordering algorithm
    • Feng XJ, Sanchis J, Reetz MT, Rabitz H (2012) Enhancing the efficiency of directed evolution in focused enzyme libraries by the adaptive substituent reordering algorithm. Chemistry 18(18):5646-5654
    • (2012) Chemistry , vol.18 , Issue.18 , pp. 5646-5654
    • Feng, X.J.1    Sanchis, J.2    Reetz, M.T.3    Rabitz, H.4
  • 8
    • 33845624902 scopus 로고    scopus 로고
    • Structure-guided SCHEMA recombination of distantly related beta-lactamases
    • Meyer MM, Hochrein L, Arnold FH (2006) Structure-guided SCHEMA recombination of distantly related beta-lactamases. Protein Eng Des Sel 19(12):563-570
    • (2006) Protein Eng des Sel , vol.19 , Issue.12 , pp. 563-570
    • Meyer, M.M.1    Hochrein, L.2    Arnold, F.H.3
  • 12
    • 84870500566 scopus 로고    scopus 로고
    • A diverse set of family 48 bacterial glycoside hydrolase cellulases created by structure-guided recombination
    • Smith MA, Rentmeister A, Snow CD, Wu T, Farrow MF, Mingardon F, Arnold FH (2012) A diverse set of family 48 bacterial glycoside hydrolase cellulases created by structure-guided recombination. FEBS J 279(24):4453-4465
    • (2012) FEBS J , vol.279 , Issue.24 , pp. 4453-4465
    • Smith, M.A.1    Rentmeister, A.2    Snow, C.D.3    Wu, T.4    Farrow, M.F.5    Mingardon, F.6    Arnold, F.H.7
  • 13
    • 4043109994 scopus 로고    scopus 로고
    • Functional evolution and structural conservation in chimeric cytochromes P450: Calibrating a structure-guided approach
    • Otey CR, Silberg JJ, Voigt CA, Endelman JB, Bandara G, Arnold FH (2004) Functional evolution and structural conservation in chimeric cytochromes P450: calibrating a structure-guided approach. Chem Biol 11:309-318
    • (2004) Chem Biol , vol.11 , pp. 309-318
    • Otey, C.R.1    Silberg, J.J.2    Voigt, C.A.3    Endelman, J.B.4    Bandara, G.5    Arnold, F.H.6
  • 14
    • 77958179580 scopus 로고    scopus 로고
    • Efficient screening of fungal cellobiohydrolase class i enzymes for thermostabilizing sequence blocks by SCHEMA structure-guided recombination
    • Heinzelman P, Komor R, Kanaan A, Romero P, Yu XL, Mohler S, Snow C, Arnold F (2010) Efficient screening of fungal cellobiohydrolase class I enzymes for thermostabilizing sequence blocks by SCHEMA structure-guided recombination. Protein Eng Des Sel 23(11):871-880
    • (2010) Protein Eng des Sel , vol.23 , Issue.11 , pp. 871-880
    • Heinzelman, P.1    Komor, R.2    Kanaan, A.3    Romero, P.4    Yu, X.L.5    Mohler, S.6    Snow, C.7    Arnold, F.8
  • 17
    • 34948815009 scopus 로고    scopus 로고
    • A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments
    • Li YG, Drummond DA, Sawayama AM, Snow CD, Bloom JD, Arnold FH (2007) A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments. Nat Biotechnol 25(9):1051-1056
    • (2007) Nat Biotechnol , vol.25 , Issue.9 , pp. 1051-1056
    • Li, Y.G.1    Drummond, D.A.2    Sawayama, A.M.3    Snow, C.D.4    Bloom, J.D.5    Arnold, F.H.6
  • 18
    • 33947216799 scopus 로고    scopus 로고
    • Diversification of catalytic function in a synthetic family of chimeric cytochrome P450s
    • Landwehr M, Carbone M, Otey CR, Li YG, Arnold FH (2007) Diversification of catalytic function in a synthetic family of chimeric cytochrome P450s. Chem Biol 14(3):269-278
    • (2007) Chem Biol , vol.14 , Issue.3 , pp. 269-278
    • Landwehr, M.1    Carbone, M.2    Otey, C.R.3    Li, Y.G.4    Arnold, F.H.5
  • 21
    • 32144432437 scopus 로고    scopus 로고
    • The swiss-model workspace: A web-based environment for protein structure homology modelling
    • Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22(2):195-201
    • (2006) Bioinformatics , vol.22 , Issue.2 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 23
    • 0029004590 scopus 로고
    • Protein modeling by e-mail
    • Peitsch MC (1995) Protein modeling by e-mail. BioTechnology 13(7):658-660
    • (1995) BioTechnology , vol.13 , Issue.7 , pp. 658-660
    • Peitsch, M.C.1
  • 24
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the Web: A case study using the Phyre server
    • Kelley LA, Sternberg MJE (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 4(3): 363-371
    • (2009) Nat Protoc , vol.4 , Issue.3 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.E.2
  • 26
    • 0038799745 scopus 로고    scopus 로고
    • General method for sequence-independent site-directed chimeragenesis
    • Hiraga K, Arnold FH (2003) General method for sequence-independent site-directed chimeragenesis. J Mol Biol 330:287-296
    • (2003) J Mol Biol , vol.330 , pp. 287-296
    • Hiraga, K.1    Arnold, F.H.2
  • 29
    • 1442286044 scopus 로고    scopus 로고
    • Using a residue clash map to functionally characterize protein recombination hybrids
    • Saraf MC, Maranas CD (2003) Using a residue clash map to functionally characterize protein recombination hybrids. Protein Eng 16(12): 1025-1034
    • (2003) Protein Eng , vol.16 , Issue.12 , pp. 1025-1034
    • Saraf, M.C.1    Maranas, C.D.2
  • 30
    • 0343621535 scopus 로고    scopus 로고
    • AAindex: Amino acid index database
    • Kawashima S, Kanehisa M (2000) AAindex: amino acid index database. Nucleic Acids Res 28(1):374
    • (2000) Nucleic Acids Res , vol.28 , Issue.1 , pp. 374
    • Kawashima, S.1    Kanehisa, M.2
  • 31
    • 0028050350 scopus 로고
    • Rapid evolution of a protein in vitro by DNA shuffling
    • Stemmer WP (1994) Rapid evolution of a protein in vitro by DNA shuffling. Nature 370(6488):389-391
    • (1994) Nature , vol.370 , Issue.6488 , pp. 389-391
    • Stemmer, W.P.1
  • 32
    • 0032518266 scopus 로고    scopus 로고
    • DNA shuffling of a family of genes from diverse species accelerates directed evolution
    • Crameri A, Raillard SA, Bermudez E, Stemmer WPC (1998) DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391:288-291
    • (1998) Nature , vol.391 , pp. 288-291
    • Crameri, A.1    Raillard, S.A.2    Bermudez, E.3    Stemmer, W.P.C.4
  • 33
    • 14844335718 scopus 로고    scopus 로고
    • Directed molecular evolution by machine learning and the influence of nonlinear interactions
    • Fox R (2005) Directed molecular evolution by machine learning and the influence of nonlinear interactions. J Theor Biol 234(2):187-199
    • (2005) J Theor Biol , vol.234 , Issue.2 , pp. 187-199
    • Fox, R.1
  • 39
    • 33748085677 scopus 로고    scopus 로고
    • Competitors want to get a piece of lipitor
    • Thayer AM (2006) Competitors want to get a piece of lipitor. Chem Eng News 84(33): 26-27
    • (2006) Chem Eng News , vol.84 , Issue.33 , pp. 26-27
    • Thayer, A.M.1
  • 40
    • 77954743785 scopus 로고    scopus 로고
    • Mutational effects and the evolution of new protein functions
    • Soskine M, Tawfik DS (2010) Mutational effects and the evolution of new protein functions. Nat Rev Genet 11(8):572-582
    • (2010) Nat Rev Genet , vol.11 , Issue.8 , pp. 572-582
    • Soskine, M.1    Tawfik, D.S.2
  • 41
    • 70349901079 scopus 로고    scopus 로고
    • Stability effects of mutations and protein evolvability
    • Tokuriki N, Tawfik DS (2009) Stability effects of mutations and protein evolvability. Curr Opin Struct Biol 19(5):596-604
    • (2009) Curr Opin Struct Biol , vol.19 , Issue.5 , pp. 596-604
    • Tokuriki, N.1    Tawfik, D.S.2
  • 42
    • 84860234014 scopus 로고    scopus 로고
    • Many pathways in laboratory evolution can lead to improved enzymes: How to escape from local minima
    • Gumulya Y, Sanchis J, Reetz MT (2012) Many pathways in laboratory evolution can lead to improved enzymes: how to escape from local minima. Chembiochem 13(7):1060-1066
    • (2012) Chembiochem , vol.13 , Issue.7 , pp. 1060-1066
    • Gumulya, Y.1    Sanchis, J.2    Reetz, M.T.3
  • 43
    • 17144364643 scopus 로고    scopus 로고
    • Maximal use of minimal libraries through the adaptive substituent reordering algorithm
    • Liang F, Feng XJ, Lowry M, Rabitz H (2005) Maximal use of minimal libraries through the adaptive substituent reordering algorithm. J Phys Chem B 109(12):5842-5854
    • (2005) J Phys Chem B , vol.109 , Issue.12 , pp. 5842-5854
    • Liang, F.1    Feng, X.J.2    Lowry, M.3    Rabitz, H.4
  • 44
    • 0037724262 scopus 로고    scopus 로고
    • Substituent ordering and interpolation in molecular library optimization
    • Shenvi N, Geremia JM, Rabitz H (2003) Substituent ordering and interpolation in molecular library optimization. J Phys Chem A 107(12):2066-2074
    • (2003) J Phys Chem A , vol.107 , Issue.12 , pp. 2066-2074
    • Shenvi, N.1    Geremia, J.M.2    Rabitz, H.3
  • 46
    • 0004315905 scopus 로고    scopus 로고
    • Biotransformations in organic chemistry
    • 6th edn. Springer, Berlin
    • Faber K (2011) Biotransformations in organic chemistry. A textbook, 6th edn. Springer, Berlin
    • (2011) A Textbook
    • Faber, K.1
  • 48
    • 27944458910 scopus 로고    scopus 로고
    • Using information theory to search for co-evolving residues in proteins
    • Martin LC, Gloor GB, Dunn SD, Wahl LM (2005) Using information theory to search for co-evolving residues in proteins. Bioinformatics 21(22):4116-4124
    • (2005) Bioinformatics , vol.21 , Issue.22 , pp. 4116-4124
    • Martin, L.C.1    Gloor, G.B.2    Dunn, S.D.3    Wahl, L.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.