Useful Programs :
You may find the following programs useful in analyzing the articles discussed during the course.
Firefox Browser: I cannot recommend this browser highly enough. The biobar extension alone makes the switch from Microsoft's ubiquitous browser a required action.
- biobar extension: Search many Bioinformatics databases from within your browser. DOWNLOAD THIS AND USE IT!
- Internet Explorer Tab: Open a web site with an Internet Explorer tab in Firefox. Useful for webpage testing or when a page just won't load in Firefox for some reason or another.
- PDF Download: Allows you to choose if you want to view a PDF file inside the browser (as PDF or HTML), if you want to view it outside Firefox with your default or custom PDF reader, or if you want to download it.
- All-in-one Sidebar: All-in-One Sidebar (AiOS) is a sidebar control, inspired by the one found in the Opera browser. Click on the left edge of your browser window to open the sidebar and get easy access to all your panels. It lets you quickly switch between sidebar panels, view dialog windows such as downloads, extensions, and more in the sidebar, or view source or websites in the sidebar.
- Awesome Screenshot: Awesome screenshot is a plugin that will allow you to "
Capture the whole page or any portion, annotate it with rectangles, circles, arrows, lines and text, blur sensitive info, one-click upload to share." It works a treat and you WILL need it in the class.
Microsoft Powertoys for Windows XP: Since you're probably stuck using Windows, here are some addons for Windows XP that can make your life infinitely easier. I routinely use the: Alt-Tab replacement, Microsoft Virtual Display Mananger, Power Calculator and Taskbar Magnifier Powertoys. If you only use one of them, in my opinion, the Virtual Disaply Manager is the one to get.
Protein Structure Visualization / Dynamics / Docking
Chimera (required for course): UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics and funded by the NIH National Center for Research Resources (grant P41-RR001081). This is the program we are using in Biochemistry II and what my own laboratory group uses for our research. Try it!
Coot/WinCOOT (required for course): Coot is a program used in the building of protein structures based on x-ray data. You can download the software here. The PDF file describing the program can be found here.
MGLTools (required for course): From the developer website: "MGLTools is a software developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures." We will use the Autodock Tools package to save our ligand as a .pdbqt file and determine the parameters of our grid box for the binding site size.
Autodock Vina (required for course): From the developer's website: "AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use." This software is straightforward to use, yet can be a very powerful tool to identify accurate binding modes of ligands to small molecules. For Windows users, I recommend downloading this Microsoft Word document and following its instructions. It will guide you in the installation 7-zip, AuDocker, Autodock Vina and MGLTools.
Update, 25 May, 2012: Another interesting set of tools I recently found for Autodock Vina is D2MD. The code for D2MD seems to be a bit cleaner than AuDocker and the package doesn't require 7-zip to open the archive.
Bioinformatics
Jalview (required for course): Jalview is a multiple alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) but is available as a general purpose alignment editor.
Text Editors
Text editors will be essential tools for you this semester as you will be editing a lot of script files and various other text documents for use in other programs. Word processing programs are not good for this task for several reasons. Both Mac OSX and Microsoft Windows ship with basic text editors, but we don't want basic. I recommend the following two programs for use during the semester.
Textpad: A text editor for Windows.
Textmate: A text editor for OSX.
Image Manipulation
Gnu Image Manipulation Program (GIMP): Need to edit images but can't afford Adobe Photoshop? Try this program out. You won't be sorry.
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