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131 results for “Molecular docking”
Figure 13 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 13 The time frame of evolution against SASA of Coumermycin complexes with SARS-CoV-2 (A) Mpro (B) PLpro (C) RdRp, during 50 ns simulation.
Figure 14 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 14 Protein interaction analysis. The green colour = hydrogen bonding, pink color = ionic interaction, grey colour = hydrophobic interaction and blue colour = water bridges showed in Coumermycin complexes with SARS-CoV-2 (A) Mpro (B) PLpro (C) RdRp during 50 ns MD simulations.
Figure 6 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 6 Molecular dynamics of Tigogenin and Gitogenin bound to aldose reductase: (a) RMSD, (b) RMSF, (c) Hydrogen bond profile; green-Tigogenin, red-Gitogenin, black-apoprotein.
Supplementary material 1 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
List of molecular weight matched decoys retrieved from DEKOIS 2.0
Figure 5 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 5 HOMO and LUMO distribution plots: (a) HOMO (b) LUMO of Tigogenin (c) HOMO (d) LUMO of Gitogenin.
Figure 4 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 4 Intermolecular interactions of (a) Tigogenin, (b) Gitogenin, (c) Epalrestat with active-site amino acids of the enzyme aldose reductase. All the ligands are shown in all atoms' green-coloured ball and stick-type representations. The names of amino acids with ID numbers are mentioned under each circle around each ligand. On the 2D figures analysis, green-coloured dotted lines indicate hydrogen bonding interactions involving electronegative elements like nitrogen and oxygen atoms; light purple-coloured dotted lines indicate π-alkyl interactions; violet-coloured dotted lines indicate π-sigma interactions. Light green colour amino acids without bonding represent van der Waals interactions, whereas, orange-red colour amino acids indicate unfavourable interactions. The light-blue halo surrounding the interacting residues represents the solvent-accessible surface that is proportional to its diameter.
Figure 1 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 1 The binding site of aldose reductase was predicted using CASTp. The residues highlighted in blue boxes constitute the binding site.
Figure 3 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 3 Analysis and comparison of the predictive power of AutoDock and AutoDock Vina: (a) Receiver operating characteristic curves, (b) Predictiveness curves, (c) Enrichment curves, red is ADock and green is Avina.
Figure 5 from: Syahputra G, Gustini N, Bustanussalam B, Hapsari Y, Sari M, Ardiansyah A, Bayu A, Putra MY (2021) Molecular docking of secondary metabolites from Indonesian marine and terrestrial organisms targeting SARS-CoV-2 ACE-2, M pro, and PL pro receptors. Pharmacia 68(3): 533-560. https://doi.org/10.3897/pharmacia.68.e68432
Figure 5 Analysis of the conformation and interaction of hydrogen bonds between ligands and receptors with a distance < 5 Å. A. ACE-2-ptilidepsin; B. PLpro -ptilidepsin; C. Mpro-ptilidepsin.
Figure 4 from: Syahputra G, Gustini N, Bustanussalam B, Hapsari Y, Sari M, Ardiansyah A, Bayu A, Putra MY (2021) Molecular docking of secondary metabolites from Indonesian marine and terrestrial organisms targeting SARS-CoV-2 ACE-2, M pro, and PL pro receptors. Pharmacia 68(3): 533-560. https://doi.org/10.3897/pharmacia.68.e68432
Figure 4 Analysis of the conformation and interaction of hydrogen bonds between ligands and receptors with a distance < 5 Å. A. ACE-2-dieckol; B. PLpro -dieckol; C. Mpro-dieckol.
Figure 2 from: Syahputra G, Gustini N, Bustanussalam B, Hapsari Y, Sari M, Ardiansyah A, Bayu A, Putra MY (2021) Molecular docking of secondary metabolites from Indonesian marine and terrestrial organisms targeting SARS-CoV-2 ACE-2, M pro, and PL pro receptors. Pharmacia 68(3): 533-560. https://doi.org/10.3897/pharmacia.68.e68432
Figure 2 The structure of the PLpro SARS-CoV-2 receptor (PDB ID: 5TL6) along with the distribution of residues on the Ramachandran plot. The PLpro receptor structure is composed of 10 α-helix structures and 19 β-sheet structures. The PLpro receptor structure is ready to use in molecular docking simulations with 96.55% of the residue in the protein-forming region.
Figure 1 from: Syahputra G, Gustini N, Bustanussalam B, Hapsari Y, Sari M, Ardiansyah A, Bayu A, Putra MY (2021) Molecular docking of secondary metabolites from Indonesian marine and terrestrial organisms targeting SARS-CoV-2 ACE-2, M pro, and PL pro receptors. Pharmacia 68(3): 533-560. https://doi.org/10.3897/pharmacia.68.e68432
Figure 1 The structure of the Mpro SARS-CoV-2 receptor (PDB ID: 6LU7) along with the distribution of residues on the Ramachandran plot. The Mpro receptor structure is composed of 10 α-helix structures and 13 β-sheet structures. The Mpro receptor structure is ready to use in molecular docking simulations with 92.15% of the residue in the protein-forming region.
Figure 3 from: Syahputra G, Gustini N, Bustanussalam B, Hapsari Y, Sari M, Ardiansyah A, Bayu A, Putra MY (2021) Molecular docking of secondary metabolites from Indonesian marine and terrestrial organisms targeting SARS-CoV-2 ACE-2, M pro, and PL pro receptors. Pharmacia 68(3): 533-560. https://doi.org/10.3897/pharmacia.68.e68432
Figure 3 Structure of the ACE 2 receptor h receptor (PDB ID: 1R42) along with the distribution of residues on the Ramachandran plot. The ACE-2 receptor structure is composed of 31 α-helix structures and six β-sheet structures. The structure of the hACE-2 receptor is ready to be used in molecular docking simulations with 98.37% of the residue in the protein-forming region.
Suppl Material- Pharmacokinetics of some newly synthesized 1, 5- benzothiazepine scaffolds: A molecular docking and molecular dynamics simulation approach
<p>It is suppl material, table and figures for publications</p>
Fig. 4 in PTP1B and α-glucosidase inhibitory activities of the chemical constituents from Hedera rhombea fruits: Kinetic analysis and molecular docking simulation
Fig. 4. Chemical structures of known compounds 7 32.
Fig. 2 in PTP1B and α-glucosidase inhibitory activities of the chemical constituents from Hedera rhombea fruits: Kinetic analysis and molecular docking simulation
Fig. 2. Key HMBC, COSY, and NOESY correlations of 1–6 and 9.
Fig. 3 in PTP1B and α-glucosidase inhibitory activities of the chemical constituents from Hedera rhombea fruits: Kinetic analysis and molecular docking simulation
Fig. 3. Experimental and calculated ECD spectra of compounds 1–4.
Fig. 3 in Serratene triterpenoids from Lycopodium cernuum L. as α-glucosidase inhibitors: Identification, structure-activity relationship and molecular docking studies
Fig. 3. SAR studies of isolates against α-glucosidase.
Fig. 2. 1H–1H in Serratene triterpenoids from Lycopodium cernuum L. as α-glucosidase inhibitors: Identification, structure-activity relationship and molecular docking studies
Fig. 2. 1H–1H COSY, Key HMBC and ROESY correlations of compounds 1–7.
Fig. 4 in Study of two isoforms of lipoxygenase by kinetic assays, docking and molecular dynamics of a specialised metabolite isolated from the aerial portion of Lithrea caustica (Anacardiaceae) and its synthetic analogs
Fig. 4. (Z)-3-(pentadec-10′-enyl)-catechol (1) and 3-pentadecylcatechol (2) Lineweaver-Burk graphs.
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International Brain Laboratory public data
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OpenNeuro
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