Verification of predicted structures of peptides using ProSA-web.

অনুরূপ উপাদানগুলি

• Z-scores from ProSA-web for AlphaFold/GalaxyRefine models of five influenza-derived CPPs. All models exhibit negative Z-scores in the native-structure range (more negatively = better), so these models are of acceptable quality to be used in dockings and molecular dynamics (MD) analysis; PB2−2 possesses the best value (−1.51) while PB1−1 possesses the worst (−0.24).
  অনুযায়ী: Sanaz Sadeh (22813266)
  প্রকাশিত: (2025)
• Time-dependent peptide–membrane interactions for PB1−1 within a POPC bilayer. The numbers of hydrogen bonds, salt bridges, and hydrophobic contacts are shown at 0, 500, and 1000 ns (4/3/2 → 2/1/8 → 4/4/3). In general, interactions become hydrophobic-dominated from polar-dominated at 0 ns to hydrophobic-dominated at 500 ns then revert back to polar dominance at 1000 ns.
  অনুযায়ী: Sanaz Sadeh (22813266)
  প্রকাশিত: (2025)
• Key contacts between CPPs and sialic acid (LSTc). This table reports, for each peptide, the contacting residues and their distances to sialic acid, resolved by interaction type (conventional H-bond, carbon H-bond, salt bridge). In every peptide, binding is mediated by polar and/or cationic residues—Lys and Arg (cationic) and Gln and Thr (polar, uncharged)—via hydrogen bonds and, where present, salt bridges.
  অনুযায়ী: Sanaz Sadeh (22813266)
  প্রকাশিত: (2025)
• HADDOCK score summary for CPP–LSTc-peptide complexes. Lower (more negative) values indicate preferred docking. PB2-1 possesses the best HADDOCK score (−47.2 ± 3.7), while PB1-1 possesses the best ΔG (−8.16 kcal/mol) as well as strongest van der Waals term (−29.9 ± 1.9 kcal/mol).
  অনুযায়ী: Sanaz Sadeh (22813266)
  প্রকাশিত: (2025)
• Structural quality metrics for refined models of the five selected CPPs (GalaxyRefiner results, CASP15 criteria). For each peptide, the top refined model’s evaluation scores are reported: GDT-HA (Global Distance Test High Accuracy), RMSD, MolProbity score, clashscore, % poor rotamers, and % Ramachandran-favored residues. Refinement improves 3D structural quality (higher GDT-HA, lower RMSD, fewer steric clashes/poor rotamers, and higher fractions of Ramachandran-favored residues). These metrics indicate that after refinement, all five peptide structures are of high 3D structural quality and reliability, suitable for detailed structural and functional analyses.
  অনুযায়ী: Sanaz Sadeh (22813266)
  প্রকাশিত: (2025)