REDCRAFT Documentation

What is REDCRAFT?

REDCRAFT is an open-source software tool for determining a protein’s structure using residual dipolar couplings (RDCs). It allows simultaneous determination of a protein’s structure and dynamics. Its effectiveness has been demonstrated on both synthetic and experimental data. REDCRAFT contains stages that allow the incorporation of user-specified dihedral angle constraints, such as those produced by TALOS or a restriction to specific regions of Ramachandran space. It is robust with respect to noise and missing data. The program is highly efficient and can produce a structure for an 80-residue protein within minutes.

GUI (v1.0) exposé

REDCRAFT Stage 1

This is the GUI view for Stage 1. The molecule we are working with here is 1a1z. Stage1 converts RDC data into .angles files. In this case, 82 new .angles files were produced, one per each residue of 1a1z.

Stage 2 Basic view

These are the basic options for Stage 2. We are mostly leaving everything default, except that the search depth is 1000 instead of the default 100.

Stage 2 Advanced view

These are the advanced options for Stage 2. We are focusing an extra depth of search on problematic residues 16 and 19 in the hopes that the true spatial configuration may be found in those deeper search depths. Additionally, we are enabling refinement, which allows floating point values for generated angles and greater precision in the PDB.

Generated protein visualization in PyMOL

After generating the intermediate PDBs for residues 1-81, we finally have a complete 82-residue PDB file for 1a1z. Using PyMOL, we can see that the protein looks correct. However, we will need to align the protein with the true 1a1z structure and inspect the RMSD to see the fit.

Comparison of alignment between the generated and true 1a1z proteins

After placing the true protein (blue) into the scene with the generated molecule (green), we aligned the molecule with align 82, 1a1z.H. The RMSD (underlined in red) represents the root mean square deviation between the two proteins, or the overall variability between the two. Here we can see that REDCRAFT has generated a molecule within only 1.6A of the true protein, only from phi/psi pairings and the sequence of amino acids!