Simple Bioinformatics Tutorial with AdK


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This tutorial provides a short introduction to basic structural bioinformatics. We will primarily use the VMD (“Visual Molecular Dynamics”) software to visualize structures and use the MultiSeq plugin [Roberts2006] for some of the bioinformatics aspects. We will also use some of the major bioinformatics databases and online tools. It is part of the ASU course PHY 542/NAN 542 — Topics in Biophysics I.

For a quick introduction on using VMD look at Protein visualization and analysis with VMD.

The tutorial is partly based on

We are looking (again) at adenylate kinase.


Analyze ligand binding residues on NMP and LID domain in adenylate kinase from an evolutionary perspective.


We are going to work through the individual sections in order. Use the navigation links in menu bar to move forward and backwards.

Learning Objectives

  • finding sequences (UniProt, BLAST)
  • structural superposition
  • protein families (PFAM)
  • multiple sequence alignment


[Roberts2006]Elijah Roberts, John Eargle, Dan Wright, and Zaida Luthey-Schulten. MultiSeq: Unifying sequence and structure data for evolutionary analysis. BMC Bioinformatics, 2006, 7:382.
[Eastwood2001]Eastwood, M.P., C. Hardin, Z. Luthey-Schulten, and P.G. Wolynes. “Evaluating the protein structure-prediction schemes using energy landscape theory.” IBM J. Res. Dev. 45: 475-497, 2001. URL:

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