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AARS Tutorial
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AARS Tutorial
Contents
Introduction
The Multiple Alignment Extension to VMD
tRNA Synthetases: Precise translation machines
Getting Started
Downloading Tutorial Files
The Aspartyl-tRNA Synthetase Aspartyl-adenylate Complex
Loading Molecules
Starting Multiple Alignment
Setting parameters for Multiple Structure Alignments
Aligning the molecules
Comparing Protein Structure And Sequence
Protein Structure
Protein Sequence
Residue Selection
Starting up Residue Selection
Exercise 1: Investigating Structure Conservation
Exercise 2: Sequence Conservation
Exercise 3: The physical meaning of Q
Summary of Results
Phylogenetic Tree
Determining Structure-based Relationships
Investigating Structural Alignment
RMSD per Residue
Pairwise RMSD
Exporting File Formats
Exporting a PDB file from user-specified selections
Exporting a multiple alignment in FASTA format
Appendices
Appendix A:
Appendix B:
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