.. -*- coding: utf-8 -*- Simple Bioinformatics Tutorial with AdK ======================================= .. Note:: Short URL for this page: https://goo.gl/vDt683 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 * `Aquaporins with the VMD MultiSeq Tool `_ (see also `TCB Bioinformatics Tutorials `_) * Roger L. Williams' `A Brief Bioinformatics Tutorial `_ We are looking (again) at adenylate kinase. Goal ==== Analyze ligand binding residues on NMP and LID domain in adenylate kinase from an evolutionary perspective. Contents ======== We are going to work through the individual sections in order. Use the navigation links in menu bar to move forward and backwards. .. toctree:: :maxdepth: 1 adk_bioinformatics multiseq msa Learning Objectives =================== - finding sequences (UniProt, BLAST) - structural superposition - protein families (PFAM) - multiple sequence alignment References ========== .. _VMD: http://www.ks.uiuc.edu/Research/vmd .. _ASU: http://asu.edu .. _`PHY 542/NAN 542 — Topics in Biophysics I`: https://becksteinlab.physics.asu.edu/learning/40/phy542-nan542-phy498-topics-in-biophysics-i .. _`Protein visualization and analysis with VMD`: https://becksteinlab.physics.asu.edu/pages/courses/2016/PHY542/practicals/vmd/ .. _MultiSeq: http://www.ks.uiuc.edu/Research/vmd/plugins/multiseq/ .. [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: http://www.research.ibm.com/journal/rd/453/eastwood.pdf Indices and tables ================== * :ref:`genindex` * :ref:`search`