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36 results for “Reaction mechanism”
The reaction mechanism for glycolysis side product degradation by Parkinson's disease-linked DJ-1
Open the record for dataset details and reuse information.
Supporting data for: The reaction mechanism of the Ideonella sakaiensis PETase enzyme
<p>Simulation data, scripts, and other supporting data for transition path sampling studies conducted as part of:</p> <p><strong>The reaction mechanism of the <em>Ideonella sakaiensis</em> PETase enzyme</strong></p> <p>By authors: Tucker Burgin, Benjamin C. Pollard, Brandon C. Knott, Heather B. Mayes, Michael F. Crowley, John E. McGeehan, Gregg T. Beckham, H. Lee Woodcock</p> <p>Published in Communications Chemistry, 2024</p> <p>This repository does not contain the aimless shooting coordinate files for each step. Those will be published separately here (for acylation) 10.5281/zenodo.10854858 and here (for deacylation) 10.5281/zenodo.10913134.</p>
Acylation shooting moves for: The reaction mechanism of the Ideonella sakaiensis PETase enzyme
<p>Shooting moves for the acylation step of the reaction mechanism of the PETase enzyme. See this repository for more information: https://doi.org/10.5281/zenodo.10854763</p>
Deacylation shooting moves for: The reaction mechanism of the Ideonella sakaiensis PETase enzyme
<p>Shooting moves for the deacylation step of the reaction mechanism of the PETase enzyme. See this repository for more information: https://doi.org/10.5281/zenodo.10854763</p>
Data Supporting "Effects of Microhydration on the Mechanisms of Hydrolysis and Cl- Substitution in Reactions of N2O5 and Seawater"
<p>All structures used in paper "Effects of Microhydration on the Mechanisms of Hydrolysis and Cl- Substitution in Reactions of N2O5 and Seawater". See README for more information.</p>
Dataset: Dissecting reaction mechanisms and catalytic contributions in flavoprotein fumarate reductases
<p>Dataset with all stationary points (in xyz file format) and videos of the reactions discussed in the work: Dissecting reaction mechanisms and catalytic contributions in flavoprotein fumarate reductases.</p>
Open Data for publication Influence of the Time Scale on the Reaction Mechanism of CO Oxidation over a Au/TiO2 Catalyst
<p>The file contains the origianl raw data for publication:</p> <p>Influence of the Time Scale on the Reaction Mechanism of CO Oxidation over a Au/TiO2 Catalyst, Angewandte Chemie, 2023</p> <p>The data contains the IR spectra of the CO2 signal, the IR spectra at different temepratures (modulation experiments) and the IR spectra for different modulation periods at 50 deg C (modulation experiments), as described in the publication.</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>
Supporting Information for the Journal Article "High-throughput ab initio reaction mechanism exploration in the cloud with automated multi-reference treatment"
<p>This dataset contains the supporting information for the journal article "High-throughput ab initio reaction mechanism exploration in the cloud with automated multi-reference treatment". It consists of two files:</p> <ul> <li>"structures.json", containing 3335 unique structures found in the exploration, and</li> <li>"energies.json", containing 2227 elementary steps and its energies found in the exploration</li> </ul> <p>In the file "structures.json", the following keys are used to characterize a structure:</p> <ul> <li> _id: the ID of the structure</li> <li>nAtoms: the total number of atoms in the structure</li> <li>atoms: the XYZ coordinates of the atoms in atomic units</li> <li>charge: the total charge of the structure</li> <li>multiplicity: the spin multiplicity 2S+1 of the structure</li> <li>label: the position of the structure on the minimum energy pathway</li> </ul> <p>In the file "energies.json", there are two major fields: structures and reactions.</p> <p>In the field "structures", the keys are:</p> <ul> <li>id: the ID of structure (can be linked to XYZ coordinates in "structures.json")</li> <li>label: the position of the structure on the minimum energy pathway</li> <li>energy_dft: PBE-D3BJ/def2-SVP total energy in atomic units</li> <li>energy_hf: HF/cc-pVDZ total energy in atomic units</li> <li>energy_ccsd: CCSD/cc-pVDZ total energy in atomic units</li> <li>energy_ccsd_t: CCSD(T)/cc-pVDZ total energy in atomic units</li> <li>energy_gibbs_correction: PBE-D3BJ/def2-SVP Gibbs free energy correction in atomic units</li> </ul> <p>In the field "reactions", the keys are:</p> <ul> <li>id: the ID of the elementary step</li> <li>lhs: the structure IDs on the left-hand side of the reaction</li> <li>rhs: the structure IDs on the right-hand side of the reaction</li> <li>type: regular or barrierless</li> <li>barrierless: binary key to indicate whether the elementary step has a barrier</li> <li>ts: ID of the transition state structure</li> <li>reaction: the ID of the reaction to which the elementary step belongs</li> </ul> <p>Due to the nature of exploration, certain structures can be explored from multiple elementary steps. Therefore, duplicated structures are common in the reaction exploration. In "structures.json", we de-duplicated the structures and only list the unique ones. The coordinates (in bohr) and global attributes like spin multiplicity and charge are provided. </p> <p>In "energies.json", each "step" represents an elementary step. 1260 of the steps are barrierless, while 967 of the steps have a barrier. The structures keys cited in "lhs", "rhs", and "ts" are before de-duplication. The "id" in each structure key points to the unique, de-duplicated structure in "structures.json".</p> <p>The main catalytical pathways (figure 9) can be found in the dataset with the following elementary_step IDs:</p> <ul> <li>62066d2fb8e290f3afb607e2</li> <li>6206704db8e290f3afb607e3</li> <li>62067db7b8e290f3afb607e4</li> <li>620a6d49b8e290f3afb607e5</li> <li>620a6dbeb8e290f3afb607e6</li> <li>620a6e2fb8e290f3afb607e7</li> <li>620a6e78b8e290f3afb607e8</li> <li>620a7f01b8e290f3afb607e9</li> <li>620a7f54b8e290f3afb607ea</li> </ul>
Mechanisms Underlying Peanut Allergic Reactions in TRACE Peanut Study Participants: Extension Study
ClinicalTrials.gov study NCT02665793. IPD Sharing: YES. Countries: 0. Publications: 1.
Characterization of the Molecular Mechanisms Involved in Delayed-Type Hypersensitivity Reactions to House Dust Mite, Diphencyprone, Nickel, and Tuberculin Purified Protein Derivative in Healthy Volunt
ClinicalTrials.gov study NCT03625219. IPD Sharing: NO. Countries: 1. Publications: 0.
Mechanism of Hypersensitivity Reactions to Iron Nanomedicines
ClinicalTrials.gov study NCT03508466. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Molecular mechanisms and potential therapeutic drugs linking to cetuximab-induced reactions in human cells
GEO Series GSE111887. Homo sapiens. 4 samples. Type: Expression profiling by array.
Molecular mechanisms and potential therapeutic drugs linking to cetuximab-induced reactions in human cells (HEK 293 cells)
GEO Series GSE111886. Homo sapiens. 2 samples. Type: Expression profiling by array.
Molecular mechanisms and potential therapeutic drugs linking to cetuximab-resistance reactions in cancer cells
GEO Series GSE114928. Homo sapiens. 6 samples. Type: Expression profiling by array.
Molecular mechanisms and potential therapeutic drugs linking to cetuximab-induced reactions in human cells (HaCaT cells)
GEO Series GSE111885. Homo sapiens. 2 samples. Type: Expression profiling by array.
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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)
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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.