Prime User Manual - ISP

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Contents
Prime 2.1 User Manual
7.8.3 Loop Refinement Options ................................................................................. 64
7.9 Technical Details for Refinement ......................................................................... 66
7.9.1 Loop Refinement............................................................................................... 66
7.9.2 Cooperative Loop Refinement .......................................................................... 67
7.9.3 Side-Chain Prediction ....................................................................................... 68
7.10 Refinement with Nonstandard Residues .......................................................... 68
7.11 Output of Refinement Jobs ................................................................................. 68
Chapter 8: Maestro Protein Structure Alignment ........................................... 71
8.1 The Protein Structure Alignment Panel............................................................... 71
8.2 The Align Binding Sites Panel .............................................................................. 74
Chapter 9: Docking Covalently Bound Ligands............................................... 77
9.1 Running Covalent Docking from Maestro........................................................... 77
9.1.1 Selecting the Ligands........................................................................................ 77
9.1.2 Defining the Ligand Reactive Groups ............................................................... 78
9.1.3 Specifying the Receptor Bond to Break ............................................................ 79
9.1.4 Specifying Receptor Residues to Sample......................................................... 79
9.1.5 Running the Job................................................................................................ 80
9.2 Running Covalent Docking from the Command Line....................................... 80
Chapter 10: Prime MM-GBSA ..................................................................................... 81
Chapter 11: Command Syntax.................................................................................... 85
11.1 blast—Run Blast Searches.................................................................................. 85
11.2 bldstruct—Build a Protein Model from an Alignment..................................... 88
11.3 fr—Fold Recognition ............................................................................................ 91
11.4 multirefine—Multi-Step Extended Sampling .................................................... 94
11.5 refinestruct—Refine a Protein Structure .......................................................... 98
11.6 ska—Protein Structure Alignment ................................................................... 102