Introduction to Bioinformatics - COIN81
COIN 81 Week Five
In this week we'll practice some protein structure modeling. There is also a lecture in the Bioinformatics Workshop, follow the link to the protein structure exercise. This is the second part of your assignment three. Most newcomers to structure modeling and visualization find it one of the most enjoyable and fascinating aspects of bioinformatics.
As you navigate each of the websites below, take a close look at the software that you can download and install for viewing. Some tools, including SWISS-MODEL, are now web-based, so you don't need to install anything. Depending on your browser settings, RasMol may launch inside MSIE. Read all terms of conditions before installing software. While the tools below are 'battle tested', you should make sure that you can uninstall / rollback if needed.
Last, make sure to have a protein or enzyme as a theme for your work, as a protein will help you keep focus, learn more, and stay organized, including using one central accession number as a link throughout the databases.
RasMol - RasMol is a very lightweight tool that allows you to view .pdb files, color chains, and display a range of views, from ball and stick to electrostatic surfaces to full molecular contours. RasMol is also used to display electronic configurations of molecules. RasMol is very easy to use, and allows GIF/JPEG image exports (nice for reports).
SWISS-MODEL workspace - is a An Automated Comparative Protein Modeling Environment - where you can upload sequences to a server for comparative analysis against known structures, and downloading best fits to your sequence. This new 'workspace' replaces a standalone application - SPDBV.
PDB - RSCB PDB is an archive of .pdb files that you'll use to download structures for viewing in RasMol or using the SWISS-MODEL workspace. PDB files are actually text files that you can open with Notepad / WordPad. Inside each PDB files are the location, identity, and position of each and every atom inside a protein.
Cn3D - Cn3D is a 'free standing' protein structure tool that you can download from NCBI. It is both easy to install and use, and has a range of features to allow viewing of chains from more than one molecule, as well as comparisons of structures. Cn3D also allows you to export images as PNG files, which you can covert to GIF/JPEG.
PubChem - PubChem is a relatively newer feature of NCBI, complete with structures of organic molecules important in bioinformatics, such as substrates. The PubChem Project allows a free text search to find organic molecules, and known physical properties from the MeSH database. See the MeSH homepage for for cross listed information.
Chime - MDL Chime is an amazing little plugin for Web browsers which allows you to see 3D views of a wide range of molecules, including organic molecules which are substrates for enzymes. You'll find this easy to install addition very useful in working with organic structures, and helpful in visualizing how biomolecules achieve various conformations.