3/18-3/25/2017: Week 6- Combining the Molecular Modelling Softwares' Benefits into a Powerful, Revised Foldit

So this week, I took some time to confirm my research into each of the three 3D modelling softwares which I have been using for molecular and protein modelling. Afterwards, I grouped the benefits of each program so that I might better lay out a road map which the Rosetta Commons may follow to modify their Foldit product so that it may be more multifaceted and applicable to a wider variety of circumstances.

Additionally, I considered some other features which I'd add given the release of the Foldit source code.

Foldit base

•3D modelling

•Default ribbon structures

•Solid molecular shapes (smallest manipulable units are amino polymer side chains)

•Collision-elimination algorithms

•Hydrophobic/hydrophilic molecules are labled

•Hydrogen bones are illustrated and their importance to protein synthesis is aptly demonstrated

Introductory protein design features

Avogadro

•Molecule construction

•Import functionality

•Range of modelling goes from atoms to full-scale molecules

•Automatic geometry correction algorithms

•Detailed imaging

•Implement the range of modelling to include Foldit ribbon structures and Avogadro ball-and-stick model via simple if statement.

PyMol

•Command line features with easy access to computer files

•Replace tool bar in Foldit

•Frame –by-frame move/playback feature and snapshot command

•Leave the UI in favor of a more aesthetically appealing one such as Avogadro or Foldit

•Combine the ideas of automatic molecule to atom viewing originating from Avogadro via simple magnification threshold addition and resulting shape change to PyMol’s Python code.

Additional features which may be added

•Pre-constructed cellular structures, such as ribosomes, with automatic re-focus feature. Since the programs deal with molecular and protein design, inserting a body hundreds of times larger than an amino acid would make the model unmanageable without auxiliary functions which automatically adjust the magnification and label all structures smaller than a few nanometers.

•An auto-play feature in which the interactions between two selected structures may be demonstrated. For example, if an amino acid chain and a ribosome are selected, the ribosome constructs a protein by accessing an online library via looking up the amino acid chain that’s entered into the ribosome. Thus, the process of protein synthesis may be illustrated with great detail. However, this would take a great deal of time and coding which may only be made available should the Rosetta commons allow access to the Foldit source code.