The following tutorials focus on sequence and structure analysis primarily through the VMD tool, Multiseq. They may also require one or more additional software packages to complete; account for the software requirements before attempting to proceed.
  • Aquaporins with the VMD MultiSeq Tool (html) (pdf, 1.9M) (required tutorial files [.tar.gz, 254M], individual files)
    For users seeking to learn about a specific use of VMD. Introduces participants to the VMD MultiSeq Tool, which links protein structures to protein sequences and allows users to compare proteins in terms of structure and sequence. The aquaporin family of membrane proteins, found in a wide range of species including humans, are used for a case study of the applications of the MultiSeq tool. Requires VMD and the VMD MultiSeq Tool. Tutorial works on Windows, Mac, and Unix/Linux platforms.

  • Evolution of Translation: Class-I aminoacyl-tRNA synthetases (pdf, 6.4 MB) (required tutorial files [tar.gz, 268 MB])
    This tutorial makes use of the MultiSeq bioinformatic analysis environment to explore the evolution of the class I aminoacyl-tRNA synthetases, which 'charge' transfer RNA (tRNA) with the correct amino acid. It is intended to be an introduction to MultiSeq, and no prior knowledge of MultiSeq is required. Topics covered include: BLAST searches, multiple sequence alignments, structural alignments, and distance-based phylogenetic trees.

  • Evolution of Translation: EF-Tu (pdf, 3.7 MB) (required tutorial files [tar.gz, 284 MB])
    This tutorial is intended to be a advanced lesson in the MultiSeq bioinformatic analysis environment, and we recommend the user first go through the Class-I Aminoacyl-tRNA synthetases tutorial prior to attempting this one. In it you will explore the evolutionary relationship of the elongation factor Tu, which ferries 'charged' tRNA from the sythetase to the ribosome. Topics covered include: profile-profile alignments, maximum likelihood phylogenetic trees with RAxML, and scripting with MultiSeq.

  • Evolution of Translation: Ribosome (pdf, 1.3 MB) (required tutorial files [tar.gz, 41 MB])
    This tutorial leads the reader through major features of the ribosome, the primary translation machinery of the cell. Interactions with the elongation factors, mRNA, and tRNA are explored, as are newly discovered 'sequence signatures' between bacterial and archaeal ribosomes. These signatures constitute much of the evolutionary distance between these two domains of life, and their role in antibiotic resistance is explored. We recommend the reader first complete the Class-I aminoacyl-tRNA synthetase tutorial prior to attempting this one.

  • Dynamical Network Analysis (pdf, 4M) (required files [tar.gz, 192M]) (network analysis code [tar.gz, 27M])
    This tutorial introduces several network analysis methods for examining dynamic signaling in biomolecular systems. The NetworkView plugin to VMD is used to display and manipulate representations of the networks projected onto the underlying molecular structures. The tutorial is designed such that it can be used by both new and experienced users of VMD, however, it is highly recommended that new users go through the "Using VMD" tutorial in order to gain a working knowledge of the program. Users will also need to download the free Carma software program for the tutorial. This tutorial should take about two hours to complete in its entirety.

  • Sequence Alignment Algorithms (pdf, 1.6M) (required tutorial files [.tar.gz, 570k], [.zip, 811k], individual files)
    Introduces participants to bioinformatics, the statistical analysis of protein sequences and structures to understand their function and predict structures when only sequence information is available. Requires Needleman-Wunsch alignment programs.Tutorial designed to work on the Mac platform only.

Tutorials and Resources

References: Emacs reference card (pdf) • Vi reference card (pdf) • Mac OSX Primer (html) (pdf) • Unix Primer (html) (pdf)
Contacts: Suggest an idea for a tutorialTutorial-l mailing listarchive of tutorial-l mailings
Case studies: water DNA lipid bilayers BPTIubiquitin myoglobinaquaporin ion channels titin lh2

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