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81 results for “Monomer”
Entropy-Driven Crystallization of Hard Colloidal Mixtures of Polymers and Monomers
<p>Data archive corresponding to the publication "Entropy-Driven Crystallization of Hard Colloidal Mixtures of Polymers and Monomers " by O. Bouzid <em>et al</em>., Polymers <strong>16</strong>, 2311 (2024). </p> <p>Preprint available at: 10.20944/preprints202407.0786.v1</p> <p>Please see README.txt for instructions on how to access and read the files from the crystallographic analysis based on the CCE norm descriptor.</p> <p>All system configurations have been generated and successively analyzed by the Simu-D software.</p> <p> </p> <p>This research was funded by MICINN/FEDER (Ministerio de Ciencia, Innovación y Universidades, Fondo Europeo de Desarrollo Regional), grant number “PID2021-127533NB-I00”, by the scholarship program from the Algerian Ministry of Higher Education and Scientific Research and by UPM and Santander Bank, “Programa Propio UPM Santander”.</p>
Structural basis of actin monomer re-charging by cyclase-associated protein
<p>1) table_of_simulations.pdf: table of simulations</p> <p>2) toppar_HIC.str: methylhistidine (HIC) topologies and parameters</p> <p> -prepared based on analogy</p> <p> -to be used with top_all36_prot.rtf and par_all36_prot.prm</p> <p>3) simulation_archive.tar.gz</p> <p> The Contents:</p> <p>1_ADP-Actin--CARP, 2_ADP-Actin--CAP1, 3_ATP-Actin--WH2, 4_ADP-Actin<br> All systems presented in the paper; see table_of_simulations.pdf<br> Each directory contains<br> 000README gromacs_topologies gromacs_tpr_files index.ndx processed_trajectories prod.mdp systems_at_t=0</p> <p>*** The rosetta models for WH2 domain and the proline-rich loop that connects it to the CARP domain can be found in 2_ADP-Actin--CAP1/rosetta_models</p> <p><br> _Topologies:<br> toppar_c36_jul16:<br> The charmm force field version used to generate topologies before conversion to gromacs; see 000README in the systems directory<br> <br> ***toppar_c36_jul16/toppar_HIC.str: The topology and parameters for methylated histidine used in the simulations.</p> <p> gromacs_topologies:<br> Contains all itp files (converted from psf file using PyTopol's psf2top utility) and parameters.<br> Note that relevant files can also be found in directories corresponding to each system ( 1_ADP-Actin--CARP 2_ADP-Actin--CAP1 3_ATP-Actin--WH2 4_ADP-Actin)</p> <p> </p>
Molecular dynamics simulation data of regulatory ACT domain monomer of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain monomer.</p> <p><strong>binding.zip</strong>: simulation starting from 21 monomer conformations with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation starting from monomer with bound Phe ligand</p> <p><strong>monomer_only.zip</strong>: simulation starting from 21 monomer conformations simulation</p> <p>Simulation setup files are also included in each folder. Adaptive sampling data are also included in <strong>monomer </strong>and <strong>binding</strong> simulations.</p> <p>Details can be found in this paper:</p> <p><strong>Yunhui Ge</strong>, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532"><em>Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</em></a> J. Biol. Chem., 2018, 293(51), pp 19532-19543</p>
Thermochemical Data for Furan-based Monomer Candidates for Frontal Ring-Opening Metathesis Polymerization (FROMP)
<p>This dataset includes 471 furan-based monomer candidates for frontal ring-opening metathesis polymerization (FROMP) and relevant thermochemistry as calculated with density functional theory (DFT). The monomer candidates were combinatorically enumerated using Diels-Alder reactions of furan derivatives as dienes and four types of dienophiles (alkenes, alkynes, allenes, and benzynes). Common substituents were enumerated for the dienophile classes, and methyl substitution on the diene was explored. We used the SMILES arbitrary target specification (SMARTS) language to produce monomers and ring-opened structures from diene and dienophile precursor SMILES, and we studied the ring-opening reaction using a homodesmotic equation with ethene. RDKit conformers were initially generated from SMILES, then optimized with GFN2-xTB. The two conformers lowest in energy were then optimized with DFT using the wb97x-D3 functional, def2-TZVP basis set, and def2/J auxiliary basis set. Gibbs free energy corrections were obtained through frequency calculations. Structures with imaginary frequencies below -50 cm^{-1} were excluded from this work, and smaller imaginary modes were flipped to be positive for free energy calculations. Modes below 50 cm^{-1} were treated with the modified rigid rotor approximation, and all thermochemical values were calculated at T=200C. The CSV file contains the monomer SMILES, the free energy of reaction for Diels-Alder addition (G_DA_200), and the enthalpy of the ring-opening reaction (H_RO_200). All energies are given in kcal/mol. An interactive HTML is also included to visualize the monomers in this dataset.</p>
Research Data for the Journal Article: Insertion of CO2 to 2-methyl furoate promoted by a cobalt hypercrosslinked polymer catalyst to obtain a monomer of CO2-based biopolyesters
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Data from: Polymerization of renewable itaconic acid in deep eutectic monomers: Effect of the quaternary ammonium cation structure
<p>The upload contains data associated with the publication, including raw data in the original file format whenever possible. Dataset content: NMR, rheology, UVVIS, FTIR, real time photo-FTIR as well as physicochemical properties of the investigated systems.</p> <p>This work was financially supported by the Lead Agency bilateral a Czech-Polish project provided by the Czech Science Foundation (21-07004K) and National Science Center Poland (CEUS-UNISONO project grant no. 2020/02/Y/ST5/00021).</p>
Control over Conformational Landscapes of Polypeptoids by Monomer Sequence Patterning
<p>This dataset accompanies the article "Control Over Conformational Landscapes of Polypeptoids by Monomer Sequence Patterning" by Audra J. DeStefano, Shawn D. Mengel, Morgan W. Bates, Sally Jiao, M. Scott Shell, Songi Han, and Rachel A. Segalman in <em>Macromolecules </em>in 2024. The article demonstrates how patterning of hydrophobic residues along a polymer backbone can tune the distribution of end-to-end distances and that these effects can be predicted by a simple bead-spring simulation. This dataset contains the necessary experimental data to reproduce the main text and supporting figures. High performance liquid chromatographs, mass spectra, double electron-electron resonance time domain signals, and simulated end-to-end distance distributions are included.</p>
Data from: A qualitative analysis of an Aβ-monomer model with inflammation processes for Alzheimer's disease
<p>We introduce and study a new model for the progression of Alzheimer's disease incorporating the interactions of Aβ-monomers, oligomers, microglial cells and interleukins with neurons through different mechanisms such as protein polymerization, inflammation processes and neural stress reactions. In order to understand the complete interactions between these elements, we study a spatially-homogeneous simplified model that allows to determine the effect of key parameters such as degradation rates in the asymptotic behavior of the system and the stability of equilibriums. We observe that inflammation appears to be a crucial factor in the initiation and progression of Alzheimer's disease through a phenomenon of hysteresis, which means that there exists a critical threshold of initial concentration of interleukins that determines if the disease persists or not in the long term. These results give perspectives on possible anti-inflammatory treatments that could be applied to mitigate the progression of Alzheimer's disease. We also present numerical simulations that allow to observe the effect of initial inflammation and concentration of monomers in our model.</p>
Photoreceptor-induced LHL4 protects photosystem II monomer - XL-MS and Alphafold2 intergrative modelling
<p>This dataset refers to the following preprint: https://www.biorxiv.org/content/10.1101/2024.02.23.581703v1 </p> <p>It provides:</p> <ul> <li>readable XL_MS annotate fragmentattion spectra for the crosslinks detected involved in the LHL4 interaction with CP43 and CP47. These complements the raw files submited in PRIDE (accession PXD049352) and the Supplementary Table 1 annexed to teh manuscript supplementray materials</li> <li>The complete output files for the AlphaFold2 multimer prediciotn of the pairwise interactions between LHL4 and CP43/CP47</li> </ul> <p> </p>
Amyloid-beta 16-22 peptide monomer simulation with the CHARMM-Drude force field and OpenMM (Run 1)
<p>Amyloid-beta 16-22 peptide (monomer) simulations with the CHARMM-Drude force field and OpenMM. This is the first independent simulation runs out of 3.</p> <p>Part 1-2 are 200 ns long, 3-8 are 100 ns each. Total trajectory length is 1 microseconds. Frame saving frequency is 10 ps.</p> <p>The system contains ~ 150 mM NaCl.</p>
Amyloid-beta 16-22 peptide monomer simulation (150 mM NaCl) with the CHARMM36m force field and Gromacs (Run 3)
<p>MD simulations of the Amyloid-beta 16-22 monomer at 150 mM NaCl concentration with CHARMM36m force field and Gromacs. This repository contains the third out of three independent runs. </p> <p>Files belong to the publication "<a href="https://doi.org/10.1021/acs.jcim.0c01063">https://doi.org/10.1021/acs.jcim.0c01063</a>"</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with Gromacs 2018.3</p> <p>Total simulation time is 500 ns. Frames are saved with 100 ps frequency. </p>
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels - full trajectories of SaFabI and EcFabI monomers and G112/113V mutants
<p>The following IDs are related to trajectories:</p> <p>v36 = EcFabI apo, monomer<br> v42 = EcFabI + TCL complex, monomer<br> v43 = EcFabI + MUT complex, monomer<br> v44 = EcFabI + AFN complex, monomer<br> v35 = SaFabI apo, monomer<br> v45 = SaFabI + TCL complex, monomer<br> v46 = SaFabI + MUT complex, monomer<br> v47 = SaFabI + AFN complex, monomer<br> v52 = G112V EcFabI apo, tetramer<br> v53 = G112V EcFabI apo, monomer<br> v54 = G113V SaFabI apo, tetramer<br> v55 = G113V SaFabI apo, monomer</p>
Data Set for Copper-Catalyzed Benzylic Functionalization of Lignin-Derived Monomers
<p>Raw NMR and HRMS data for the article entitled Copper-Catalyzed Benzylic Functionalization of Lignin-Derived Monomers. The folder names corrspond to the compound names. </p>
Data from: A qualitative analysis of an Aβ-monomer model with inflammation processes for Alzheimer’s disease
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Data from: Regulation of the formin INF2 by actin monomers and calcium-calmodulin
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Control over Conformational Landscapes of Polypeptoids by Monomer Sequence Patterning
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Data from: A monomer-dimer switch modulates the activity of plant adenosine kinase
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Neutron Reflectometry data and code for the manuscript entitled: 'Enrichment of charged monomers explains non-monotonic polymer volume fraction profiles of multi-stimulus responsive copolymer brushes'
<p>Contained in the zip file is the reduced neutron reflectometry data, the code used to analyse the data and jupyter notebooks used implement this code. Data is for proposal number PP4274, experiment number PPR6490 on the Platypus Reflectometer at ANSTO, Australia. The data is name with measurement numbers. The attached excel document describes the condition which corresponds to measurement number. </p>
Additional simulation data of α-synuclein monomer
<p>This dataset includes data for the article entitled "The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds". </p>
Amyloid-beta 16-22 peptide monomer simulation with the CHARMM-Drude force field and OpenMM (Run 2)
<p>Amyloid-beta 16-22 peptide (monomer) simulations with the CHARMM-Drude force field and OpenMM. This is the second independent simulation runs out of 3.</p> <p>Part 1-2 are 200 ns long, 3-8 are 100 ns each. Total trajectory length is 1 microseconds. Frame saving frequency is 10 ps.</p> <p>The system contains ~ 150 mM NaCl.</p>
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Allen Brain Atlas
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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.