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691 results for “Molecular dynamics”
Figure 5 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 5 2D poses of (A) Novobiocin; (C) Clorobiocin; (B) hydroxychloroquine; (D) N3; docked into the active site of SARS-CoV-2 main protease.
Figure 9 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 9 (A) surface map (B) 2D poses showing ligand interactions of Coumermycin; docked into the active site of SARS-CoV-2 RNA-dependent RNA polymerase (PDB: 7bv2).
Figure 4 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 4 (A) Structure of standard inhibitor of SARS-CoV-2 main protease, N3, (B) 2D pose for the interaction of hydroxychloroquine into the active site of SARS-Cov-2 main protease enzyme.
Figure 8 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 8 (A) surface map (B) 2D poses showing ligand interactions of Coumermycin; docked into the active site of SARS-CoV-2 papain-like protease (PDB: 6wx4).
Figure 10 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 10 The RMSD plot of Coumermycin complex with SARS-CoV-2 (A) Mpro (B) PLpro (C) RdRp, at 50 ns simulation.
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.
research data supporting "Revealing the organization of catalytic sequence-defined oligomers via combined molecular dynamics simulations and network analysis"
<p>This repository contains all the data generated and analyzed including the starting structures, the input files, the trajectory files, the output data from cpptraj and network analyses, and in-house scripts used to prepare the network and module files shown in the paper <strong>"Revealing the organization of catalytic sequence-defined oligomers via combined molecular dynamics simulations and network analysis"</strong> published in <strong>Journal of Chemical Information and Modeling</strong> (DOI: 10.1021/acs.jcim.2c00101). </p>
Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations
<p>Raw simulations of the deacylation step by PETase on a PET dimer model substrate, ran with CP2K 6.1 software at the PBE:AMBER level. Details can be found in the original manuscript (<a href="https://doi.org/10.1021/acscatal.1c03700">https://doi.org/10.1021/acscatal.1c03700</a>): Molecular topology in AMBER Parameter Topology format and Trajectories in CHARMM binary coordinate format DCD.</p> <p>QM RESIDUE LIST:<br> GLY57<br> TYR58<br> SEP131<br> MET132<br> TRP156<br> ASP177<br> SER178<br> ILE179<br> ALA180<br> HID208<br> WAT6290<br> WAT6318<br> WAT7630</p> <p>VMD selection:<br> (name CA C O HA2 HA3 and resname GLY and resid 57) or (name N CA CB H HA HB2 HB3 and resname TYR and resid 58) or (name O2 C3 O3 C4 O4 C5 O5 O6 C7 O7 C8 C9 C10 C11 C12 C13 C14 C15 C16 H5 H6 H7 H12 H13 H14 H15 H16 H17 H18 H19 H20 and resname SEP and resid 131) or (name N CA SD CE CB CG H HA HB2 HB3 HG2 HG3 HE1 HE2 HE3 and resname MET and resid 132) or (name CB CG CD1 CD2 CE2 CE3 NE1 CZ2 CZ3 CH2 HB2 HB3 HD1 HE1 HE3 HZ2 HZ3 HH2 and resname TRP and resid 156) or (name CG OD1 OD2 CB HB2 HB3 and resname ASP and resid 177) or (name C O and resname SER and resid 178) or (name N CA C O CG2 CD1 CB CG1 H HA HB HG12 HG13 HG21 HG22 HG23 HD11 HD12 HD13 and resname ILE and resid 179) or (name N CA CB H HA HB1 HB2 HB3 and resname ALA and resid 180) or (name CB CG CD2 ND1 CE1 NE2 HB2 HB3 HD1 HD2 HE1 and resname HID and resid 208) or (name O H1 H2 and resname WAT and resid 6290) or (name O H1 H2 and resname WAT and resid 6318) or (name O H1 H2 and resname WAT and resid 7630)</p> <p>PYMOL selection:<br> (name CA+C+O+HA2+HA3 & resn GLY & resi 57) | (name N+CA+CB+H+HA+HB2+HB3 & resn TYR & resi 58) | (name O2+C3+O3+C4+O4+C5+O5+O6+C7+O7+C8+C9+C10+C11+C12+C13+C14+C15+C16+H5+H6+H7+H12+H13+H14+H15+H16+H17+H18+H19+H20 & resn SEP & resi 131) | (name N+CA+SD+CE+CB+CG+H+HA+HB2+HB3+HG2+HG3+HE1+HE2+HE3 & resn MET & resi 132) | (name CB+CG+CD1+CD2+CE2+CE3+NE1+CZ2+CZ3+CH2+HB2+HB3+HD1+HE1+HE3+HZ2+HZ3+HH2 & resn TRP & resi 156) | (name CG+OD1+OD2+CB+HB2+HB3 & resn ASP & resi 177) | (name C+O & resn SER & resi 178) | (name N+CA+C+O+CG2+CD1+CB+CG1+H+HA+HB+HG12+HG13+HG21+HG22+HG23+HD11+HD12+HD13 & resn ILE & resi 179) | (name N+CA+CB+H+HA+HB1+HB2+HB3 & resn ALA & resi 180) | (name CB+CG+CD2+ND1+CE1+NE2+HB2+HB3+HD1+HD2+HE1 & resn HID & resi 208) | (name O+H1+H2 & resn WAT & resi 6290) | (name O+H1+H2 & resn WAT & resi 6318) | (name O+H1+H2 & resn WAT & resi 7630)</p>
Basket-type G-Quadruplex with Two Tetrads in the Presence of TMAO and Urea: A Molecular Dynamics Study
<p>Molecular Dynamics simulation trajectories of basket-type DNA G-quadruplex (PDB: 2KF7). The structures have been simulated in the temperatures 300 K and 360 K in pure water, 1 M TMAO solution, 2 M urea solution and the mixture of 1 M TMAO and 2 M urea.</p> <p> </p>
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.
Data From: Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations
<p>This dataset contains MD simulation results for CCR5 receptor in different states. There are three states this GPCR could be in: 1.apo state, i.e. not bound to any other protein or ligand 2.holo state, i.e. bound by maraviroc (MRV) 3.GP120 bound state, i.e. bounded to HIV envelope protein GP120 and human receptor CD4. </p> <p>For apo state simulations, three different starting structure were used and the simulation results for them are given in three different folders named after the PDB ID of initial structures. </p> <p>One critical residue of CCR5 receptor, GLU283, was considered in two different protonation state, hence there are two folders for each studied system, GLU283 and GLH283 for differently protonated systems. </p> <p>The MD trajectories of studied systems are in dcd format and due to size issues waters, ions and membrane atoms were removed. </p> <p>For each system, three replica MD simulations were performed, hence, there are three folders with names REPLICA1, REPLICA2, REPLICA3.</p> <p> </p>
"Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host-guest systems"
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Data For Hybrid Monte-Carlo Molecular Dynamics Methods For Estimation of Solidus and Liquidus Compositions, a Case Study in Cu-Ni and Au-Si
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Effect of pre-twinning on deformation behavior of [0001]-textured nanocrystalline Mg: a molecular dynamics study
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