Pymol - molecular visualization system
Avagodro - Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Rosetta - you can think of rosetta as a suite of "movers" that do specific tasks. These movers can be combined in various ways to do proteins structure prediction and design!

Rosetta today exists in a couple different forms:
  • Rosetta apps
    • This is the traditional Rosetta, where each "app" or "protocol" is a standalone hard-coded pipeline of movers that performs a specific task given a set of input flags. Some examples include:
      • Relax - repacks and minimizes the input pdb
      • Score - scores the input structure
      • AbinitioRelax - given a sequence and a set of fragments, does de novo structure prediction, followed by relax.
    • c++ knowledge is required to write your own apps. 
  • RosettaScripts
    • RosettaScripts is an app where the pipeline is not hard-coded but instead be controlled through an input XML script. Many of the basic movers (such as mutate or repack etc) along with more advanced protocols (such has hybridize or remodel etc.) can be accessed through RosettaScripts. Today many rosetta developers no longer build standalone rosetta apps, but instead develop "movers" that can be accessed and controlled in fine detail through rosettascripts and XML scripting.
  • Pyrosetta (will not be covered in workshop)
    • Pyrosetta is a python wrapper around rosetta movers. Allowing you to write python "apps" just as you would with c++. It is often used to prototype apps/protocols before rewriting them in c++.  Check out:
  • Foldit
    • Yet another form of Rosetta is FOLDIT. Foldit is a GAME, yet its is also a powerful standalone program.  The tool is extensively used to make manual tweaks to designs. You can Relax (aka wiggle all), you can mutate (aka design), you can rebuild part of structure... you can invoke many rosetta app protocols in Foldit using human-friendly names

Subpages (2): Foldit Rosetta Energy