Fig. 3: Six examples of models built by AF2 and D-AF. | Communications Biology

Fig. 3: Six examples of models built by AF2 and D-AF.

From: Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints

Fig. 3

Detailed evaluation results are available in Supplementary Data 1 and 2. For each example, three structures are shown: the native structure (green), the superimposed model by AF2 (cyan) to native(green), and the superimposed model by D-AF (magenta) to native(green); a The Nop5p subunit of fibrillarin/Nop5p complex (PDB: 1NT2, chain: B, 258 amino acids). AF2 RMSD: 11.83 Å, D-AF RMSD: 2.28 Å. b CbnR subunit from a LysR family transcriptional regulator (PDB:1IXC, chain:A, 295 amino acids). AF2 RMSD: 16.33 Å, D-AF RMSD: 1.96 Å. c The LarsR protein of LasR-Aqs1 complex from Pseudomonas aeruginosa (PDB: 6V7W, chain: B, 239 amino acids). AF2 RMSD: 18.69 Å, D-AF RMSD: 2.18 Å. d Single MgsA protomer with three domains of the E. coli MgsA protein (PDB: 3PVS, chain: A, 447 amino acids), AF2 RMSD: 17.63 Å, D-AF RMSD: 3.07 Å. e The Raf1 subunit from assembly of RuBisCO (PDB: 6KKN, chain: A, 376 amino acids), AF2 RMSD: 17.90 Å, D-AF RMSD: 5.42 Å; f A protein of two tandem RNA recognition motifs of Human antigen R (PDB: 4EGL, chain: A, 177 amino acids), AF2 RMSD: 13.73 Å, D-AF RMSD: 7.83 Å.

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