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Useful Programs :

You may find the following programs useful.

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.

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.

Protein Structure Visualization

VMD: Visual Molecular Dynamics, is a protein visualization program that allows you to examine files from the PDB in much greater depth. It also serves as a front end to the molecular dynamics program NAMD which we have on the departmental cluster. It is free and fairly intuitive to use. TheWindows installer file for the latest version (1.5.6) can be found here. The Mac OSX installer DMG file for Intel x86 based Macintosh computers can be found here.

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.

Here's a link to a two page command list for UCSF's Chimera molecular graphics program.

Pymol: From the website: "PyMOL is a molecular viewer, render tool, and 3D molecular editor developed in the spirit of RasMol and OpenRasMol and intended for visualization of 3D chemical structures including atomic resolution X-ray crystal structures of: proteins, nucleic acids (DNA, RNA, & tRNA), and carbohydrates, as well as small molecule structures of drug leads, inhibitors, metabolites, sugars, nucleoside phosphates, and other ligands including inorganic salts and solvent molecules. PyMOL serves academic research and education in chemistry and biology, and the biotechnology and pharmaceutical industries by rendering publication-quality journal illustrations of macromolecules including drug targets such as GPCRs, kinases (Abl, Raf, Aurora, EGFR), proteases (HIV, BACE, Factor Xa), phosophorylases (PTP1B), and other enzyme targets, as well as therapeutic biomolecules such as humanized antibodies, cytokines, hormones, and serpins. Available molecular representations for nanotechnology pictures include space-filling "CPK" atoms, chemical bonds, cartoon ribbons, molecular surfaces, and solvent accessible surface meshes". Pymol is used by many structural biology labs and while it takes some time learning the commands, it is very powerful and worth the effort.

DeepView: Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

Protein Structure Determination or Refinement

CCP4: A suite of programs used to determine the crystallographic structure of a macromolecules. Contains everything you need to go from diffraction data to final structure validation. Have a look at the wiki here.

CNS: Crystallographic and NMR System. Another software suite the allows the determination and refinement of macromolecular structures from x-ray diffraction or NMR data.

Coot: Crystallographic Object Oriented Toolkit. It is a program for the building and refinement of crystallographic structures.

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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