Useful Programs :

You may find the following programs useful during the course.

Firefox Browser: I cannot recommend this browser highly enough. The bioFOX extension alone makes the switch from Microsoft's ubiquitous browser a required action. Chrome is great, but it doesn't have the functionality that Firefox does, so I recommend using Firefox.

• BioBar extension: A great exntension for Firefox that gives you access to nearly every bioinformatic database you'd ever need. Install this add-on 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.

Dexpot: (Free) Virtual desktop manager for Windows. This program brings the X11 multiple desktop experience to windows. Get this program. Have a look at the website and see what the program can do for you, you will not be sorry. I use this program on my Windows laptops and am very happy with it.

Protein Structure Visualization

Chimera: From the UCSF Chimera website: 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. I'm learning to use it and the more time I spend with it, the more I like it.

A two page command list for UCSF's Chimera molecular graphics program.

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.

Chemical Drawing Programs

Marvinsketch: MarvinSketch allows users to quickly draw molecules through basic functions on the GUI and advanced functionalities such as sprout drawing, customizable shortcuts, abbreviated groups, default and user defined templates and context sensitive popup menus. You must register to download and use the software.

Molecular Docking Software

Autodock Vina: Autodock Vina is a freely available moelcular docking program that determines the lowest energy poses for small molecule ligands docked into protein structures. It is fast, simple to use and runs on Windows, OSX and Linux platforms.

PyRx: PyRx is, among other things, a graphical front end for Autodock Vina. It can be used to rapidly setup, run and evaluate the results of an Autodock Vina calculation. The Windows version can be downloaded here and the OSX version can be found here.

Sequence Analysis and Alignment

UGene: UGene is an open-source bioinformatics program that will allow you to analyze sequences, perform multiple sequence alignments and construct phylogenetic trees. It runs on MacOS, Windows and Linux.