Thesis Title: Subtitle - NMR Spectroscopy Research Group

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120 Chapter 4. Protein Structure Determination from Pseudocontact Shifts using ROSETTA. Figure S4.2 Improved fragment assembly by PCS-ROSETTA. Fragments were assembled in 10000 different runs of CS-ROSETTA (red), 10000 different runs of PCS-ROSETTA (black), and 10000
4.8 Supporting information. 121 different runs using exclusively the PCS score of PCS-ROSETTA (blue). The plots show the frequency with which structures of different C rmsd values to the target structure were found. The red and black solid lines reproduce the data of Figure 4.2. The dashed lines show the corresponding data obtained in independent calculations that included the full atom refinement step. The same colors were used for calculations with and without the full atom refinement step. The full atom refinement step does not significantly change the C rmsd of the structures produced in the fragment assembly step with respect to the target structure. The targets are labeled A-J as in Table 4.1. Figure S4.3 Energy landscape generated by CS-ROSETTA and PCS-ROSETTA, with full atom ROSETTA energies and C α rmsd values being calculated using only the core residues as defined in Table S4.1. A to J: full atom ROSETTA energies plotted versus the C α rmsd to the target structure for structures calculated using CS-ROSETTA. A’ to J’: Combined ROSETTA energy and PCS score plotted versus the C rmsd to the target structure for structures calculated using PCS-ROSETTA. The lowest energy structures are indicated in red. The targets are labeled A-J as in Table 4.1.
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Computational study of proteins wit
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iii Schmitz C, Stanton-Cook MJ, Su
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v Acknowledgements I would like to
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vii Keywords paramagnetic nmr, pseu
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ix 2.3.3 Manual resonance assignmen
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xi List of Figures Figure 1.1 NMR e
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xiii
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xv List of Abbreviations α Subunit
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2 Chapter 1. Introduction. The scal
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4 Chapter 1. Introduction. In contr
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6 Chapter 1. Introduction. as the c
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8 Chapter 1. Introduction. Figure 1
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28 Chapter 2. Possum: paramagnetica
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Page 95 and 96: 3.5 Algorithm. 79 rhombic component
Page 97 and 98: 3.6 Program Features. 81 each fitti
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Page 103 and 104: 3.7 Study case. 87 The coordinates
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Page 109 and 110: 3.9 Acknowledgment. 93 variables, t
Page 111 and 112: 3.10 References. 95 Galassi M, Davi
Page 113 and 114: 3.11 Supporting information. 97 Zwe
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Thesis Title: Subtitle - NMR Spectroscopy Research Group

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