Development and Application of Novel ... - Jacobs University

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6.6. References ......................................................................................................................................... 167 Supporting information ............................................................................................................................. 170 Summary and outlook................................................................................................................................. 184 Curriculum vitae ix
PART I: CAPDE Chapter 1 Computer-Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering 1.1. Abstract The combination of computational and directed evolution methods has proven a winning strategy for protein engineering. We refer to this approach as computer-aided protein directed evolution (CAPDE) and the chapter summarizes the recent developments in this rapidly growing field. We will restrict ourselves to overview the availability, usability and limitations of web servers, databases and other computational tools proposed in the last five years. The goal of this chapter is to provide concise information about currently available computational resources to assist the design of directed evolution based protein engineering experiment. 1.2. Background Protein engineering comprises a large number of techniques applied to evolve or design protein with desired function.[1] The primary objective in any protein engineering experiment is to identify specific sequence changes and alter the protein for desired 1
Page 1 and 2: Development and Application of Nove
Page 3 and 4: Funding The work described in this
Page 5 and 6: Abstract In the last decades, enzym
Page 7 and 8: Table of Content Acknowledgement ..
Page 9: 4.5. References ...................
Page 13 and 14: PART I: CAPDE of protein structure
Page 15 and 16: PART I: CAPDE In this chapter, for
Page 17 and 18: PART I: CAPDE library size and rand
Page 19 and 20: PART I: CAPDE 1.4. Evolutionary con
Page 21 and 22: PART I: CAPDE The web server perfor
Page 23 and 24: PART I: CAPDE based MSA a protein s
Page 25 and 26: PART I: CAPDE name or structure and
Page 27 and 28: PART I: CAPDE for experimental scre
Page 29 and 30: PART I: CAPDE characterizes it bind
Page 31 and 32: PART I: CAPDE stability using inter
Page 33 and 34: PART I: CAPDE in the protein using
Page 35 and 36: PART I: CAPDE Table 1.4: Summarizin
Page 37 and 38: PART I: CAPDE in which the volume o
Page 39 and 40: PART I: CAPDE 21. Chica RA, Doucet
Page 41 and 42: PART I: CAPDE 44. Knoll M, Hamm TM,
Page 43 and 44: PART I: CAPDE 69. Vangone A, Spinel
Page 45 and 46: PART I: CAPDE 95. Emekli U, Schneid
Page 47 and 48: PART I: CAPDE 119. Parthiban V, Gro
Page 49 and 50: PART I: MAP 2.0 3D 2.2. Introductio
Page 51 and 52: PART I: MAP 2.0 3D improve the fitn
Page 53 and 54: PART I: MAP 2.0 3D ⎛ 0.0 9.70 19.
Page 55 and 56: PART I: MAP 2.0 3D amino acid (α)
Page 57 and 58: PART I: MAP 2.0 3D of transformatio
Page 59 and 60: PART I: MAP 2.0 3D amino acid oxida
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PART I: MAP 2.0 3D aliphatic amino
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PART I: MAP 2.0 3D Figure 2.5, char
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PART I: MAP 2.0 3D Figure 2.5: Chem
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PART I: MAP 2.0 3D 2.4.2. Phytase P
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PART I: MAP 2.0 3D Figure 2.6: MAP
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PART I: MAP 2.0 3D Figure 2.7: Amin
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PART I: MAP 2.0 3D active site resi
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PART I: MAP 2.0 3D (δ(282)Q→ch =
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PART I: MAP 2.0 3D 11. Turner NJ (2
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PART I: MAP 2.0 3D 36. Liao GJ, Lee
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PART II: MD Simulation Chapter 3 In
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PART II: MD Simulation Force field
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PART II: MD Simulation Electrostati
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PART II: MD Simulation 3.4. Structu
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PART II: MD Simulation where vi and
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PART II: P450BM-3 Reductase Domain
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PART II: P450BM-3 HEME/FMN Complex
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PART II: P450BM-3 HEME/FMN & CoSep
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In the second part of the thesis, m
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Curriculum vitae Personal Details N
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Statutory Declaration I, RAJNI VERM
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