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. Author manuscript; available in PMC: 2023 Feb 6.
Published in final edited form as: Curr Opin Struct Biol. 2023 Jan 6;78:102526. doi: 10.1016/j.sbi.2022.102526

Figure 2. Alphafold structure prediction and comparison with experimental data.

Figure 2

(A) Alphafold2 prediction [18] of a segment of a viral polyprotein (Gen-Bank accession, HQ389543, amino acids 480-1253) shown in ribbon representation. Predictions are coloured from red (worst) to blue (best) according to pLDDT values. Three (mainly blue) clearly defined domains of secondary structure (Zinc binding domain, Macro domain and Helicase) are separated by linkers with low-confidence scores. The terminii are marked with their corresponding amino acid numbers.

(B) Middle domain of AF prediction for the viral polyprotein (amino acids 802-945) used as a query to find a similar structure in the PDB, giving the high scoring hit (green, PDB ID 3GPQ, TM-score 0.78 [21]), including the ligand__A-__A.

(C) An overlay of the structure of PDB ID 3GPQ with the Alphafold2 prediction (blue) of the second domain shown in Figure 2A. The similar three dimensional structures imply that ligand binding details available from experimental data can provide molecular modelling template(s) for ligand/drug design on the predicted protein. Foldseek [21] was for the database search of crystal structures. Maestro[53] and Pymol[54] were used for creating the figures.