Figure 3
The Cα RMSD distributions of the structures generated by MSA-MD and the structural alignments with the native structure.
The structures formed by the 10 ns MSA-MD compared with their own native structures of the seven peptides. White structure is the native conformation and the yellow structure is the best structure formed by MSA-MD. (A) The Cα RMSD distribution of the structures formed by MSA-MD simulations relative to the ALPHA1 crystal structure and the overlay of the best predicted structure with the ALPHA1 native structure. (B) The Cα RMSD distribution of the structures formed by MSA-MD simulations relative to the 1L2Y crystal structure and the overlay of the best predicted structure with the 1L2Y native structure. (C) The Cα RMSD distribution of the structures formed by MSA-MD simulations relative to the PolyAla crystal structure and the overlay of the best predicted structure with the standard conformation. (D) The Cα RMSD distribution of the structures formed by MSA-MD simulations relative to the 1UAO crystal structure and the overlay of the best predicted structure with the 1UAO native structure. (E) The Cα RMSD distribution of the structures formed by MSA-MD simulations relative to the 1E0Q crystal structure and the overlay of the best predicted structure with the 1E0Q native structure. (F) The Cα RMSD distribution of the structures formed by MSA-MD simulations relative to the 1ERD crystal structure and the overlay of the best predicted structure with the 1ERD native structure. (G) The Cα RMSD distribution of the structures formed by MSA-MD simulations relative to the 1GAB crystal structure and the overlay of the best predicted structure with the 1GAB native structure.
