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Results of molecular dynamics simulation. (A) RMSD variation curve; (B) fluctuation of amino acid residues; (C) Rg curve; (D) SASA fluctuation curve; (E) Number of H bonds. RMSD, root mean square deviation; RMSF, root mean square fluctuation; Rg, gyration; SASA, solvent-accessible surface area; H-bonds, hydrogen bonds.

Journal: Molecular Medicine Reports

Article Title: Dihydroalterperylenol from endophytic fungus Alternaria semiverrucosa and its antitumour activity uncovered by transcriptome analysis, molecular docking and molecular dynamics simulations

doi: 10.3892/mmr.2025.13740

Figure Lengend Snippet: Results of molecular dynamics simulation. (A) RMSD variation curve; (B) fluctuation of amino acid residues; (C) Rg curve; (D) SASA fluctuation curve; (E) Number of H bonds. RMSD, root mean square deviation; RMSF, root mean square fluctuation; Rg, gyration; SASA, solvent-accessible surface area; H-bonds, hydrogen bonds.

Article Snippet: LH and ZH were responsible for the application and implementation of the Molecular dynamics simulation software.

Techniques: Solvent

Molecular dynamics simulation energy analysis. (A) Energy contribution of each amino acid residue in the protein-ligand complex (BMP2-1rew); (B) Total binding energy of the protein-ligand complex (BMP2-1rew); (C) Energy contribution of each amino acid residue in the protein-ligand complex (ID1-6mgn); (D) Total binding energy of the protein-ligand complex (ID1-6mgn); (E) Energy contribution of each amino acid residue in the protein-ligand complex (TGIF2-2dmn); (F) Total binding energy of the protein-ligand complex (TGIF2-2dmn).

Journal: Molecular Medicine Reports

Article Title: Dihydroalterperylenol from endophytic fungus Alternaria semiverrucosa and its antitumour activity uncovered by transcriptome analysis, molecular docking and molecular dynamics simulations

doi: 10.3892/mmr.2025.13740

Figure Lengend Snippet: Molecular dynamics simulation energy analysis. (A) Energy contribution of each amino acid residue in the protein-ligand complex (BMP2-1rew); (B) Total binding energy of the protein-ligand complex (BMP2-1rew); (C) Energy contribution of each amino acid residue in the protein-ligand complex (ID1-6mgn); (D) Total binding energy of the protein-ligand complex (ID1-6mgn); (E) Energy contribution of each amino acid residue in the protein-ligand complex (TGIF2-2dmn); (F) Total binding energy of the protein-ligand complex (TGIF2-2dmn).

Article Snippet: LH and ZH were responsible for the application and implementation of the Molecular dynamics simulation software.

Techniques: Residue, Binding Assay

Free energy landscape of molecular dynamics simulation. (A) BMP2-1rew; (B) ID1-6mgn and (C) TGIF2-2dmn. RMSD, root mean square deviation

Journal: Molecular Medicine Reports

Article Title: Dihydroalterperylenol from endophytic fungus Alternaria semiverrucosa and its antitumour activity uncovered by transcriptome analysis, molecular docking and molecular dynamics simulations

doi: 10.3892/mmr.2025.13740

Figure Lengend Snippet: Free energy landscape of molecular dynamics simulation. (A) BMP2-1rew; (B) ID1-6mgn and (C) TGIF2-2dmn. RMSD, root mean square deviation

Article Snippet: LH and ZH were responsible for the application and implementation of the Molecular dynamics simulation software.

Techniques: