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Dataset results
16 results for “Molecular Mechanics simulations”
Dataset from "Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations"
<p>Dataset from "Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations", containing the most relevant simulation output trajectories ran with GROMACS 2021:</p> <p>1) apo simulations, including wildtype, Y28F, and H228A;<br> 2) holo simulations, including the two tested protonation states for the antibiotic;<br> 3) mutant simulations, including Y18F, H228A, E268Q, and E284Q.</p> <p>All folders contain the topology file (.top), restraint files (.itp), the initial coordinates file (.gro), and the coordinates after the first minimization (em1.gro). The output trajectories of all replicas (per system) have been concatenated in a single compressed file (.xtc).</p>
Molecular dynamics trajectories obtained from simulations of mechanically-controlled break-junctions and associated zero-bias conductance.
<p>This data set contains structural information and the associated zero-bias conductance of mechanically-controlled break-junction experiments. It contains:</p> <ul> <li>Six (multi) xyz files (trajectory_0X.xyz), which contain different trajectories produced by molecular dynamic simulations (using <a href="https://www.lammps.org/">LAMMPS</a> and <a href="https://docs.lammps.org/Packages_details.html#pkg-reaxff">reactive force fields</a>) of a mechanically-controlled break-junction. These simulations start from a gold wire with attached molecules. One side of the wire is slowly pulled away, until the gold wire is broken apart and a molecular junction is formed. The outermost six layers of the goldwire are frozen in the simulation. The temperature of the simulation was set to 300K.</li> <li>Six files (transmission_0X.dat) with the calculated zero-bias conductance (G/G<sub>0</sub>). Each entry corresponds to the zero-bias conductance of the corresponding structure from the xyz files. The zero-bias conductance was calculated using non-scc DFTB+, as, e.g., described <a href="https://dftbplus-recipes.readthedocs.io/en/latest/transport/carbon2d-trans.html">here</a>.</li> </ul> <p>For more information see dx.doi.org/XXXXXXX.</p>
Source Data for the paper: "Quantum-classical simulations reveal the photoisomerization mechanism of a prototypical first-generation molecular motor"
<p>This dataset contains the raw data for the results shown in the paper.</p> <p>For each figure of the paper (main text), one directory with data file(s) is provided.</p>
trajectories for: Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations
<p>Coarse-grained trajectories produced and analysed for publication: </p> <p>----------------------</p> <p>Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations</p> <p>Andreas Haahr Larsen*, Lilya Tata*, Laura John & Mark S.P. Sansom</p> <p>Department of Biochemistry, University of Oxford, Oxford, United Kingdom, OX1 3QU</p> <p>PLOS comp biol (in press) </p> <p>-------------------------</p> <p> </p> <p>** file overview**</p> <p>md_X.xtc: (X=0..14) 15 repeated CG simulations (1500 ns each) of the FYVE domain from EEA1 binding to POPC:POP1 bilayer. The repeats differ in the rotation of the initial frame.<br> </p> <p>final_cg2at_aligned.pdb: initial frame for AT (after CG2AT)</p> <p>prod_cym_cent_repX.xtc (X=1,2,3) 3 repeated AT sims (500 ns each) of the FYVE domain from EEA1 binding to POPC:POP1 bilayer. </p> <p>** scripts for reproduction at GitHub**</p> <p>scripts and files for reproduction are available at: https://github.com/andreashlarsen/Larsen-Tata2021-FYVE</p>
All-atom simulations elucidate the molecular mechanism underlying RNA-membrane interactions
<p>Topology files and frames extracted from the minimum of the free energy profile F(d_z) (or F(d_min) for single-stranded RNAs), within 2.5kBT. These files can be used to reproduce the hydrogen bond analyses in the manuscript.</p> <p>Scripts which were used to extract hydrogen bond information are available on <a href="https://github.com/salvatoredimarco/rna-membrane">https://github.com/salvatoredimarco/rna-membrane</a></p> <p><strong>Systems:</strong></p> <p>4xN: nucleosides</p> <p>4xN2: dinucleotides</p> <p>4xN3: trinucleotides</p> <p>4xN_OPC: nucleosides simulated with OPC water model. Energy threshold is here 1.0*kBT, because of weaker binding.</p> <p>1xGA, 1xGU, 1xGC, 1xCU</p> <p>1xGGC, 1xGCG</p> <p>1xquadruplex: G-quadruplex</p> <p>1xstrand: 19-mer RNA strand</p> <p>1xhairpin: 16-mer folded hairpin</p> <p>1x16mer_elong: 16-mer unfolded, restrained</p> <p>2x16mer_loose1/2: 16-mer unfolded, unrestrained</p>
Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations
<p>Raw simulations of the acylation 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>RESIDUE LIST:<br> GLY57<br> TYR58<br> SER131<br> MET132<br> TRP156<br> ASP177<br> SER178<br> ILE179<br> ALA180<br> HID208<br> MOL262</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 CA C O OG CB HA HB2 HB3 HG and resname SER 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 H HA 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 C1 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C2 C20 C3 C4 C5 C6 C7 C8 C9 H1 H10 H11 H12 H13 H14 H15 H16 H17 H2 H3 H4 H5 H6 H7 H8 H9 O1 O2 O3 O4 O5 O6 O7 O8 O9 and resname MOL and resid 262)</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 CA+C+O+OG+CB+HA+HB2+HB3+HG & resn SER & 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+H+HA & resn ALA & resi 180) | (name CB+CG+CD2+ND1+CE1+NE2+HB2+HB3+HD1+HD2+HE1 & resn HID & resi 208) | (name C1+C10+C11+C12+C13+C14+C15+C16+C17+C18+C19+C2+C20+C3+C4+C5+C6+C7+C8+C9+H1+H10+H11+H12+H13+H14+H15+H16+H17+H2+H3+H4+H5+H6+H7+H8+H9+O1+O2+O3+O4+O5+O6+O7+O8+O9 & resn MOL & resi 262)</p>
Molecular Dynamics (MD) Simulation Data for Dynamics Underlie the Drug Recognition Mechanism by the Efflux Transporter EmrE
<p>MD simulations on the proton bound (PDB 8UWU), deprotonated on E14A (PDB 8UWU), TPP Bound (PDB 8UWU) on our NMR derived structures.</p> <p> </p> <p>MD simulations on the proton bound (7MH6) and deprotonated on E14A (7MH6) on X-ray structures. </p> <p> </p> <p>Total raw simulation data would be too large for uploading to repositories. To reduce size of file, starting structure and tpr files are uploaded. Final structure at 2.5 μs are also uploaded. </p>
Molecular Simulation Elaborating the Structural Mechanism of Spiri forming nitrilase from Bacillus safensis
<p><span>Nitrilases are indispensable in the biocatalytic hydrolysis of nitrile compounds, which presents promising applications in industrial biocatalysis and environmental remediation. In this study, we conduct an extensive investigation into the structural and functional properties of <em>Bacillus safensis </em>nitrilase (<em>BsNIT</em>), highlighting its assembly, substrate binding mechanisms, stability, evolutionary relationships, and active site conservation. Using a combination of molecular modeling and extensive molecular dynamics simulations, we unveil the intricate architecture of <em>BsNIT</em>, which exhibits a left-handed spiri-forming structure stabilized by interchain interactions and salt-bridge formations. The substrate-binding pocket, surrounded by aromatic residues, displays multifaceted accessibility through distinct channels. Our simulations reveal substrate-specific catalytic orientations, with glutaronitrile and 4-cyanobutanoic acid displaying stable binding, while benzonitrile exhibits a propensity for rapid product diffusion. Analysis of active site conservation emphasizes the functional significance of preserved catalytic residues, providing insights into <em>BsNIT</em>'s catalytic efficiency. This comprehensive study offers a thorough understanding of <em>BsNIT</em>'s structure-function relationships, paving the way for future advancements in enzyme engineering and bioremediation strategies targeting nitrile pollutants.</span></p>
Molecular mechanism underlying SNARE-mediated membrane fusion enlightened by all-atom molecular dynamics simulations
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Molecular dynamics simulations reveal the selectivity mechanism of structurally similar agonists to TLR7 and TLR8
<p>Trajectory, topology and index files for TLR7 (apo), TLR7-R, TLR7-H, TLR7-G, TLR8 (apo), TLR8-R, TLR8-H, TLR8-G systems. </p>
Experimental and Simulation data for the molecular mechanism of temperature-dependent phase separation of HSF1
<p>1. lmp_datatfile</p> <p>The documents contain the LAMMPS input datafiles of initial configuration used to run all simulations, including single chain, trimer(LZ1-3-RD), and RD systems.</p> <p>2.Experimental data.</p> <p>The documents contain original ucsf data</p>
MD_Simulations_Molecular_mechanisms_of_inorganic-phosphate_release_from_the_core_and_barbed_end_of_actin_filaments
<p>This repository contains the models, protocols, datasets and Jupyter notebooks to reproduce the computational experiments in the paper:</p> <p>"Molecular mechanisms of inorganic-phosphate release from the core and<br> barbed end of actin filaments"</p> <p>by W. Oosterheert, F.E.C Blanc, A. Roy, A. Belyy, M.B. Sanders,, O. Hofnagel, G. Hummer, P. Bieling, S. Raunser</p>
Datasets associated with the manuscript "Discovering SARS-CoV-2 neoepitopes and the associated TCR-pMHC recognition mechanisms by combining single-cell sequencing, deep learning, and molecular dynamics simulation techniques"
<p>meta_data_TCR-pMHC_from_STCRDab.tsv, TCR-pMHC structures used for contacts analysis.</p><p>tcr_gliph_input_sars2.tsv, input files (TCR sequences and related information) used for clustering TCRs targeting SARS-CoV-2 epitopes and epitope-unknown TCRs.</p><p>tcr_gliph_input_non-sars2.tsv, input files used for clustering TCRs targeting non-SARS-CoV-2 epitopes and epitope-unknown TCRs.</p><p>tcr_gliph_output*, output files from the GLIPH software, including the recognized TCR clusters by GLIPH (convergence-group.txt), the linkage information of TCR clusters (clone-network.txt), and the recognized motif in TCR clusters (kmer.txt).</p><p>md_trajs.tar, structures and MD simulation trajectories of TCR-614-pMHC and TCR-204-pMHC complexes.</p>
Exploring Conformational Landscapes and Binding Mechanisms of Convergent Evolition for the SARS-CoV-2 Spike Omicron Variant Complexes with the ACE2 Receptor Using AlphaFold2-Based Structural Ensembles and Molecular Dynamics Simulations
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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>
Molecular Dynamics simulation data for the article "Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism"
<p>Zipped archives with MD simulation data for the article "Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism" (eLife, accepted).</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.