Protein 3D Structure Computed from Evolutionary Sequence Variation (original) (raw)
Figure 2
Predicted 3D structures for three representative proteins.
Visual comparison of 3 of the 15 test proteins (others in Figure S3) reveals the remarkable agreement of the predicted top ranked 3D structure (left) and the experimentally observed structure (right). Center: Cα-RMSD error and, in parentheses, number of residues used for Cα-RMSD error calculation, e.g., 2.9 Å Cα-RMSD (67). The ribbon representation was chosen to highlight the overall topographical progression of the polypeptide chain, rather than atomic details such as hydrogen bonding (colored blue to red in rainbow colors along the chain, N-term to C-term; helical ribbons are α-helices, straight ribbons are β-strands, arrow in the direction of the chain; each structure in front and back view, related by 180 degree rotation). The predicted proteins can be viewed in full atomic detail in deposited graphics sessions for the Pymol program (Web Appendix A4) or from their coordinates (Web Appendix A).