Thesis Title: Subtitle - NMR Spectroscopy Research Group

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122 Chapter 4. Protein Structure Determination from Pseudocontact Shifts using ROSETTA. Figure S4.4 Identification of successful calculations with PCS-ROSETTA. The quality factor Q reports on the agreement between the experimental and calculated PCS. A value below 20% usually indicates that the calculated structure satisfy the PCS restraint. Above 25%, the quality of the structure is poor. On the y axis are the average C α rmsd calculated between the lowest scored structure and the next four lowest scoring structures. Rmsd below 3 Å are indicative of the convergence of the protocol. Convergence criterion and quality factor can be combined to further ascertain the success of the calculations for the targets A-B-C-D-E-F-I-G., and reject targets H and J. The targets are labeled A-J as in Table 4.1. The values are those of Table 4.1-h for the x axis, and Table 4.1-g for the y axis.
4.8 Supporting information. 123 Figure S4.5 Flow diagram of PCS-ROSETTA. (a) Fragments are selected by their chemical shifts using CS-ROSETTA. (b) The PCS weight is calculated using equation (4.4) on 1000 decoys generated with CS-ROSETTA. (c) Structures are produced by the classical fragment assembly of ROSETTA with addition of the PCS-score. (d) Side chains are added to the structures and subjected to a full atom minimization. (e) Resulting structures are rescored using a combination of the ROSETTA full atom energy score and the PCS score. (f) Best structures are selected by their lowest score.
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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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28 Chapter 2. Possum: paramagnetica
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Page 95 and 96: 3.5 Algorithm. 79 rhombic component
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Page 101 and 102: 3.6 Program Features. 85 Carlo prot
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
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Thesis Title: Subtitle - NMR Spectroscopy Research Group

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