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393 results for “Molecular dynamics simulations”
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>
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>
AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants : Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance
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Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study- PART 6
<p>Trajectories and input files of the simulations of the S151T Rbfox*·pre-miR20b* system.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study- PART 1
<p>Simulations of the Rbfox protein.</p> <p> </p>
Dataset for molecular dynamics simulations of coalescence of Pd and AuPd clusters
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Molecular dynamics simulation trajectories of homorepeat peptides
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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>
Simulation trajectories from ab-initio molecular dynamics of 4x4x4 super cell of Li3OCl with 4 Li concentrations
<p>Lithium-rich oxychloride antiperovskites are promising solid electrolytes for enabling next-generation batteries. Here, we report a comprehensive study varying Li<sup>+</sup> concentrations in Li<sub>3</sub>OCl using <em>ab-initio</em> molecular dynamics simulations. The simulations accurately capture the complex interactions between Li<sup>+</sup> vacancies (V'<sub>Li</sub>), the dominant mobile species in Li<sub>3</sub>OCl. The V'<sub>Li</sub> polarize and distort the host lattice, inducing additional non-vacancy mediated diffusion mechanisms and correlated diffusion events that reduce the activation energy barrier at concentrations as low as 1.5% V'<sub>Li</sub>. Our analyses of discretized diffusion events Li in both space and time illustrate the critical interplay between correlated dynamics, polarization, and local distortion in promoting ionic conductivity in Li<sub>3</sub>OCl.</p>
data for "An unbound proline-rich signaling peptide frequently samples cis conformations in Gaussian accelerated molecular dynamics simulations"
<p>Disordered proline-rich motifs are common across the proteomes of many species and are often involved in protein-protein interactions. Proline is a unique amino acid due to the covalent bond between the backbone nitrogen and the proline side chain. The resulting five-membered ring allows proline to sample the <em>cis</em> state about its peptide bond, which other residues cannot do as readily. Because proline-rich disordered sequences exist as ensembles that likely include structures with the proline peptide bond in <em>cis</em>, a robust methodology to accurately account for these conformations in the overall ensemble is crucial. Observing the <em>cis </em>conformations of proline in a disordered sequence is challenging both experimentally and computationally. Nitrogen-hydrogen NMR spectroscopy cannot directly observe proline residues, which lack an amide bond, and computational methods struggle to overcome the large kinetic barrier between the <em>cis </em>and <em>trans </em>states, since isomerization usually occurs on the order of seconds. In the current work, Gaussian accelerated molecular dynamics was used to overcome this free energy barrier and simulate proline isomerization in a tetrapeptide (KPTP) and in the 12-residue proline-rich SH3 binding peptide, ArkA. We found that Gaussian accelerated molecular dynamics, when combined with a lowered peptide bond dihedral angle potential energy barrier (15 kcal/mol), allowed sufficient sampling of the proline <em>cis </em>and <em>trans </em>states on a microsecond timescale. All ArkA prolines spend a significant fraction of time in <em>cis</em>, leading to a more compact ensemble with less polyproline II helix structure than an ArkA ensemble with all peptide bonds in <em>trans</em>. The ensemble containing <em>cis</em> prolines also matches more closely to <em>in vitro</em> circular dichroism data than the all-<em>trans</em> ensemble. The ability of the ArkA prolines to isomerize likely affects the peptide’s ability to bind its partner SH3 domain, and should be studied further. This is the first molecular dynamics simulation study of proline isomerization in a biologically relevant proline-rich sequence that we know of, and a similar protocol could be applied to study multi-proline isomerization in other proline-containing proteins to improve conformational diversity and agreement with <em>in vitro</em> data.</p>
Molecular dynamics simulations of BmrA starting from X-ray and cryo-EM structure
<p>This archive contains all the MD trajectories presented in the article<br> 'Drug-bound and -free outward-facing structures of a multidrug ABC exporter point to a swing mechanism'<br> by Chaptal et al,<br> https://doi.org/10.1101/2021.03.12.435132</p> <p><br> MD simulations of the BMRA Xray structure:<br> - 4 replicates with short equilibration:<br> BMRA_Xray_run1<br> BMRA_Xray_run2<br> BMRA_Xray_run3<br> BMRA_Xray_run4 <br> - 2 replicates with long equilibration:<br> BMRA_Xray_run5<br> BMRA_Xray_run6</p> <p>MD simulations of the BMRA Cryo-EM:<br> - 4 replicates with short equilibration:<br> BMRA_Cryo_run1<br> BMRA_Cryo_run2<br> BMRA_Cryo_run3<br> BMRA_Cryo_run4<br> - 2 replicates with long equilibration:<br> BMRA_Cryo_run5<br> BMRA_Cryo_run6</p> <p>MD simulations of BMRA + R6G:<br> BMRA_R6G_run1<br> BMRA_R6G_run2<br> BMRA_R6G_run3</p> <p> </p>
Molecular dynamics simulation data of stapled peptides
<p>Molecular dynamics simulations for Axin and HIV peptides.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.