This blog post introduces a new tool for Foldit protein design. The Blueprint Panel displays the amino acid sequence and secondary structure of your protein. By default, each letter of the sequence is colored according to the φ and ψ torsions at that position in the structure, following the same ABEGO coloring scheme used by the Rama Map. Above the sequence, a secondary structure diagram reflects the sheet and helix assignment at each position. The Auto Structures button will detect sheets and helices, and make the appropriate secondary structure assignments.
The Blueprint panel is accompanied by the Building Blocks panel. Building blocks represent discrete patterns of protein backbone that can be applied to your protein structure. The building blocks provided here correspond to specific loops that are frequently observed in natural proteins (they were previously known as "Ideal Loops" in the Rama Map). All building blocks are meant to connect secondary structure elements directly, with a sheet or helix on either side. The appropriate use of a building block is dependent on this secondary structure "context." For example, a Helix-Sheet building block would make a good connection between a helix at position 20 and a sheet at position 23, but would not work well if the helix and sheet positions were reversed.
Click-and-drag a building block onto the Blueprint panel to apply the building block to your structure. Applied building blocks will remain outlined in the Blueprint panel. Applied building blocks will continue to exert torsional constraints wherever they are placed—these constraints behave like rubber bands for φ and ψ torsions, and will try to keep residues close to the original building block shape whenever you use Wiggle.
Click-and-drag a building block off of the Blueprint panel to remove the building block; this will also remove the associated torsional constraints. It is recommended that you leave building blocks and torsional constraints in place while you continue to fold a protein.
The Building Block panel includes two special building blocks next to the Context menu: one block is all-helix and another is all-sheet. These special building blocks can be placed on the Blueprint panel to shape residues into ideal helices and ideal sheets. They do not exert torsional constraints, and disappear immediately after they are applied.
The Blueprint Panel will be enabled in specific design puzzles. It can be accessed from the Actions menu in the Original Interface, or from the Main menu in the Selection Interface. Try it out now in Puzzle 1305!( Posted by bkoep 70 548 | Thu, 10/27/2016 - 22:14 | 0 comments )