Desmond Tutorial

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<strong>Desmond</strong> <strong>Tutorial</strong> Preparing Proteins with Missing Residues or Side Chains Figure 3.6 Prime Find Homologs window Click the ‘Import’ button to read in the truncated 1su4 protein structure file so it can be used as a self-template. Now it is time to ʹfoolʹ Prime. Instead of reading the structures of sequence homologues to be used as structural templates—as we would do for comparative modeling—we will read in the truncated 1su4 protein structure file so it can be used as a self‐template. e. Click Import under Find Homologs. The Import Homolog From PDB File window appears as shown in Figure 3.7. Figure 3.7 Import Homolog From PDB File window in Prime Locate and select the truncated 1su4 protein structure file that has the missing residues. Click the ‘Import’ button. f. Select the truncated 1su4 protein structure file that has the missing residues from the Files area. In this example, it is the 1su4_missing_loop.pdb file which was manually altered to remove residues 132–136. Click Import. 34 D. E. Shaw Research September 2008
Preparing Proteins with Missing Residues or Side Chains Running Prime The Structure Prediction window reappears as shown in Figure 3.8. There is a single yellow line in the Homologs area of the window that shows quality measures for the sequence alignment. Since this is essentially a self‐alignment, the sequence identity is 100%. If you click the left tip of the yellow line (which is in the ID column), you see the sequence alignment at the top of the panel. The sequence alignment and the incomplete structure in the workspace are color coded by residue type. Figure 3.8 Sequence alignment in the Prime Structure Prediction window Since we performed a selfalignment, the sequence identity is 100%. Click Next. g. Click Next. The next phase in the process is Edit Alignment. Since this is self‐alignment, we do not need to perform this step. Click Next again. Note that Prime may pop up a warning message, but ignore it. At this point Build Structure is highlighted in the workflow diagram at the bottom of the window as shown in Figure 3.9. September 2008 D. E. Shaw Research 35
Page 1 and 2: Desmond Tutorial Desmond Version 2.
Page 3 and 4: Preface Intended Audience This tuto
Page 5 and 6: from outermost to innermost, separa
Page 7 and 8: Contents Preface . . . . . . . . .
Page 9 and 10: Loading Files from the Command Line
Page 11 and 12: List of Figures Figure 1.1: Simulat
Page 13 and 14: 1 Desmond Tutorial Introducing Desm
Page 15 and 16: Desmond Tutorial Tutorial Steps Fig
Page 17 and 18: Desmond Tutorial Tutorial Steps 3.
Page 27 and 28: Desmond Tutorial Tutorial Steps Sys
Page 31 and 32: 2 Learning the Maestro- Desmond Env
Page 33 and 34: Learning the Maestro-Desmond Enviro
Page 41 and 42: 3 Preparing Proteins with Missing R
Page 43 and 44: Preparing Proteins with Missing Res
Page 45: Preparing Proteins with Missing Res
Page 55 and 56: 4 Preparing a Desmond simulation wi
Page 57 and 58: Preparing a Desmond simulation with
Page 69 and 70: 5 Finishing Preparations for Desmon
Page 71 and 72: Finishing Preparations for Desmond
Page 77 and 78: 6 Running Desmond Simulations Overv
Page 79 and 80: Running Desmond Simulations Running
Page 81 and 82: 7 Preparing Free Energy Perturbatio
Page 83 and 84: Preparing Free Energy Perturbation
Page 93 and 94: 8 Visualization and Analysis using
Page 95 and 96: Visualization and Analysis using Ma
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9 Analyzing Trajectories Using VMD
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Analyzing Trajectories Using VMD Lo
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Analyzing Trajectories Using VMD Ge
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Analyzing Trajectories Using VMD Ge
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Analyzing Trajectories Using VMD An
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Analyzing Trajectories Using VMD Bi
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10 Documentation Resources Detailed
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