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534 results for “scaffold”
Molecular datasets from "SMILES-Based Deep Generative Scaffold Decorator for De-Novo Drug Design"
<p>Herein find the molecular datasets from "<a href="https://chemrxiv.org/articles/SMILES-Based_Deep_Generative_Scaffold_Decorator_for_De-Novo_Drug_Design/11638383">SMILES-Based Deep Generative Scaffold Decorator for De-Novo Drug Design</a>". These were generated with SMILES-based scaffold decorator generative models trained with two training sets (DRD2 and ChEMBL). These generative models require a partially-built molecule (scaffold) as input and output several possible completions for each scaffold. Each dataset corresponds to a model trained with the ChEMBL or DRD2 sets, wither multi-step (ms) or single-step (ss) and the provenance of the scaffolds (validation set, or non-dataset).</p> <p>The molecules generated are annotated with a set of descriptors. The DRD2 datasets have the predicted probability of each molecule to be active on DRD2 (p) obtained from a Random Forest model. The ChEMBL model's descriptors are related to the synthesizability of the molecules (see manuscript). Also, the datasets decorated from validation set scaffolds are annotated whether they are part of the validation set (in_validation).</p>
Test datasets for Hi-C scaffolding
<p>We provided two datasets for testing Hi-C scaffolding tools. For the CHM13 test dataset, we randomly chunked the first 10Mb of chr1, chr2 and chr3 of the T2T-CHM13v1.1 human genome assembly (Nurk et al. 2022) into 57 contigs. The Hi-C data downloaded from the telomere-to-telomere consortium GitHub repository (https://github.com/marbl/CHM13) were mapped to the reference genome and the reads mapped to these regions were extracted to generate Hi-C alignment files. For the LYZE01 test dataset, the Saccharomyces cerevisiae strain W303 genome assembly (Matheson et al. 2017) was split at positions with gaps (‘N’) to get the original contigs. An independent Hi-C data library was downloaded from the NCBI repository (GEO Accession GSM2417297) and downsampled to approximately 20X. The downsampled Hi-C data were mapped to the contigs to generate Hi-C alignment files.</p> <p>We provided five files for each test dataset: the contig file in FASTA format, the FASTA index file generated with SAMtools faidx command, and the Hi-C alignment file in BAM format sorted by coordinate, in BAM format sorted by query names (with the identifier 'qn' in the file name), and in BED format.</p>
Siloxide tripodal ligands as a scaffold for stabilizing lanthanides in the +IV oxidation state
<p>This upload contains raw data (NMR, X-Ray, EPR, Cyclic Voltammetry, UV, IR, Magnetism) files for the article</p>
Extended data for Manuscript: Identification of potential biological targets of oxindole scaffolds via in silico repositioning strategies
<p>This is the Extended Data for the manuscript "<strong>Identification of potential biological targets of oxindole scaffolds via <em>in silico</em> repositioning strategies" </strong>submitted to F1000 Research.</p> <p>Extended Data include a list of all the accession codes as mentioned in the text, the results of 2D fingerprint-based similarity analyses and ligand-protein complexes predicted by rigid docking and Induced Fit Docking calculations.</p>
Synthesis of an anion receptor using 3,6-diaminophenanthrene as a scaffold
<p>1H and 13C NMR spectra for the compounds:</p> <ul> <li>2-iodo-4-nitrobenzoic acid (<strong>6</strong>)</li> <li>(2-iodo-4-nitrophenyl)methanol (<strong>7</strong>)</li> <li>2-iodo-4-nitrobenzaldehyde (<strong>8</strong>)</li> <li>5,5'-dinitro-[1,1'-biphenyl]-2,2'-dicarbaldehyde (<strong>9</strong>)</li> <li>3,6-dinitrophenanthrene (<strong>10</strong>)</li> <li>3,6-diaminophenanthrene (<strong>11</strong>)</li> <li>1,1'-(phenanthrene-3,6-diyl)bis(3-(3,5-bis(trifluoromethyl)phenyl)urea) (<strong>13</strong>)</li> </ul> <p>MNOVA files for the compounds are provided, as well as the original files recorded on a 400MHz JEOL NMR spectrometer in jdf format.</p>
Figures - Vat photopolymerization of biomimetic bone scaffolds based on Mg, Sr, Zn-substituted hydroxyapatite: Effect of sintering temperature
<p>Figures of publication "<span>Vat photopolymerization of biomimetic bone scaffolds based on Mg, Sr, Zn-substituted hydroxyapatite: Effect of sintering temperature</span>".</p> <p><a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.ceramint.2024.05.038" target="_blank" rel="noreferrer noopener"><span><span>https://doi.org/10.1016/j.ceramint.2024.05.038</span></span></a></p>
Set of images published in publication "Cleaning strategies for 3D-printed porous scaffolds used for bone regeneration fabricated via ceramic vat photopolymerization"
<p>Figures of publication "Cleaning strategies for 3D-printed porous scaffolds used for bone regeneration fabricated via ceramic vat photopolymerization".</p> <p><a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.ceramint.2024.10.160" target="_blank" rel="noreferrer noopener"><span><span>https://doi.org/10.1016/j.ceramint.2024.10.160</span></span></a></p>
Drug-unique scaffolds
<p>A list of 221 drug-unique scaffolds that represented approved drugs but were not detected in currently available bioactive compounds is provided. For each scaffold, the corresponding approved drug(s) are listed with their IDs in DrugBank and names. The structures of scaffolds and drugs are provided in canonical SMILES representation.</p>
Analog series-based scaffolds from ChEMBL with associated activity information
<p>Reported is the activity information for the 12,294 analog series-based (ASB) scaffolds extracted from ChEMBL database. For each ASB scaffold structural and activity information for all analogs comprising the analog series is provoded. </p>
Research data supporting "Pericyte seeded dual peptide scaffold with improved endothelialization for vascular graft tissue engineering"
<p>Raw research data supporting the paper:</p> <p>Campagnolo, P. <em>et al</em>., Pericyte seeded dual peptide scaffold with improved endothelialization for vascular graft tissue engineering, 2016, Advanced Healthcare Materials, 5(23), 3046-3055.</p> <p> </p>
Research data supporting "Electrospun aniline-tetramer-co-polycaprolactone fibres for conductive, biodegradable scaffolds"
<p>Research data supporting the publication: Guex, A.G. et al., 2017, "Electrospun aniline-tetramer-<em>co</em>-polycaprolactone fibres for conductive, biodegradable scaffolds", MRS Communications. https://doi.org/10.1557/mrc.2017.45</p> <p> </p>
Smart 3D super-resolution microscopy reveals the architecture of the RNA scaffold in a nuclear body
<p>Data associated with the article "Smart 3D super-resolution microscopy reveals the architecture of the RNA scaffold in a nuclear body". A README.txt is provided that explains the data provided.</p>
spaceRAT Scaffolds
<p>This is a list of prebuilt scaffolds available in the <a href="https://github.com/shdam">spaceRAT R package. </a><br><br>An <a href="https://services.healthtech.dtu.dk/shiny/sohdam/ShinyRAT/">R Shiny app</a> is (soon) available to interact and project samples into the scaffolds available in spaceRAT. Instructions to run the Shiny app locally can be found <a href="https://github.com/shdam/ShinyRAT">here</a>.</p><p>All scaffolds are described in the <a href="https://github.com/shdam/spaceRATScaffolds">spaceRATScaffolds R data package</a>.</p>
Micro-CT image of cell-populated collagen scaffold in the aqueous environment (contrasted with PTA)
<p>A dataset of the collagen scaffold populated with the 3T3 cells scanned in the aqueous environment using Bruker Skyscan 1276 machine (Bruker, Belgium). </p><p><strong>Scaffold production</strong></p><p>The processes of obtaining and working with collagen scaffolds were conducted in an isolated environment under sterile conditions. The collagen sponge matrix was manufactured at the Center for Collagen Innovation within the Institute of Regenerative Medicine at Sechenov University and provided to us for experimental purposes. In order to obtain the collagen, the authors utilized animal-derived materials sourced from the tendons of large horned cattle. To do this, the tendons were cleaned of excess tissues, cut into pieces with a thickness of 0.5-1 cm, and sequentially treated for 12 hours in a 0.5 M NaCl solution. Subsequently, the mass was homogenized in a 0.83 M acetic acid solution. The resulting suspension was hydrolyzed with 0.24% pepsin for 2 days, after which 1 M NaOH was added to adjust the pH to 7.5, halting the hydrolysis process. The suspension was precipitated with a 12% NaCl solution, the resulting precipitate was redissolved in 0.02 M acetic acid, and then dialyzed. To obtain collagen porous matrices (sponges), the obtained solution was neutralized using 0.1 M NaOH until a pH of 7-7.5 was reached, and the resulting suspension was lyophilized at -40°C for 2 days.</p><p>Subsequently, the collagen matrix was cut into cubes with sides measuring 0.5 cm. These cubes were placed in 15 ml test tubes filled with 70% ethyl alcohol for sterilization. The test tubes were then placed on a shaker and left in the refrigerator at +4°C for 24 hours. Afterward, the collagen matrices were removed from the alcohol and rinsed five times with 0.9% NaCl.</p><p>Following the alcohol rinse to confirm the absence of toxicity, an elution test, adapted following the ISO 10993 protocol, was conducted. To obtain collagen cube extracts, they were incubated in a cell culture medium at a volume of 1 ml per sample for 24 hours at 37°C. The 3T3 cell culture was passaged, with 5000 cells seeded in each well of a 96-well plate. After 24 hours, the cells were treated with extract at a volume of 200 µl per well and left in the incubator at 37°C for 24 hours. The following day, extracts were collected, and AlamarBlue reagent (Invitrogen, Waltham, MA, USA) was added according to the manufacturer's instructions to assess the metabolic activity of the cells. Serial dilutions of sodium dodecyl sulfate (SDS) were used as the positive control. Fluorescence intensity was measured using a Victor Nivo spectrofluorimeter (PerkinElmer, Waltham, Massachusetts, USA) at an excitation wavelength of 530 nm and an emission wavelength of 590 nm.</p><p><strong>Cell seeding</strong></p><p>After confirming the absence of cytotoxic effects, collagen sponges were seeded with the NIH 3T3 cell line at a density of 50,000 cells per sample (cubes of collagen sponge measuring 0.5 cm per side). </p><p><strong>Staining technique</strong></p><p>Fixed specimens in 10% formalin with PBS were washed after 24 hours with distilled water and after that placed in 3% phosphotungstic acid dissolved in distilled water for 24 hours and kept on the rotary shaker at room temperature. After staining, samples were washed and stored in distilled water at 5 °C. </p><p><strong>Image acquisition and reconstruction</strong></p><p>A plastic tube filled with distilled water containing the contrasted sample was placed on the sample holder in a SkyScan 1276 micro-CT (Bruker, Kontich, Belgium) and were scanned at 3 μm voxel resolution with 70 kV voltage and 200 uA source power and an aluminum filter with 1 mm of thickness. The rotation was set to 360° around the vertical axis of the sample, with two middle frames for each 0.2° angle step.</p><p>After scanning, the data were reconstructed using Bruker's NRecon software. During reconstruction, the ring artifact reduction value was set to 20% and the beam hardening correction value to 30%. After that, samples were exported as a series of 16-bit TIFF images which could be opened in the specialized software. </p>
Proteomic data sets after selecting mitochondrial proteins from the scaffold software for Ingenuity Pathway analysis (IPA Qiagen)
<p>List of fold change proteomic data sets of dFCM- 39 vs. 12Day and105 vs. 12Day, cFCM- 40 vs. 12Day and115 vs. 12Day , mouse heart 90 vs. 1 day after selecting mitochondrial proteins from the scaffold software for Ingenuity Pathway Analysis (IPA Qiagen)</p>
Collection of analog series-based (ASB) scaffolds
<p>The entire collection of 23,791 unique ASB scaffolds generated from compounds from Probes and Drugs Portal (PDP) and ChEMBL (version 23) is reported. Each ASB scaffold is provided in canonical SMILES representation, the database origin (DB_origin) is specified, and the number of analogs (#analogs) the scaffold represents reported. In addition, for each ASB scaffold from ChEMBL, unique target annotations of corresponding analogs are provided using UniProt target identifiers. For ASB scaffolds from PDP, collected compound annotations are provided. For scaffolds shared between PDP and ChEMBL the number of analogs is provided in the form 'X|Y' where 'X' and 'Y' denote the number of analogs in PDP and ChEMBL, respectively. Scaffolds are rank-ordered according to the number of analogs they represent. </p>
Collection of analog series-based (ASB) scaffolds shared between ZINC, ChEMBL, and PubChem
<p>Analog series-based (ASB) scaffolds shared between ZINC and ChEMBL (version 22), ZINC and PubChem and all the three databases are provided as three separate files. For each ASB scaffold, the SMILES representation of ZINC compounds is provided. In addition, the number of ZINC compounds, the number and the list of targets it was annotated with is reported. A README file is also given.</p>
Evaluating porous protein microcrystals as a capture scaffold for nucleic acids
<p>Curated data for manuscript titled "Evaluating porous protein microcrystals as a capture scaffold for nucleic acids," by A.A. Jones, M. Masri, K. Horak, and C. D. Snow.</p>
Data for the paper: The Role of Glycerol in Manufacturing Freeze-Dried Chitosan and Cellulose Foams for Mechanically Stable Scaffolds in Skin Tissue Engineering
<p>The Dataset contains all the data, described in the article "<strong>The Role of Glycerol in Manufacturing Freeze-Dried Chitosan </strong><br><strong>and Cellulose Foams for Mechanically Stable Scaffolds in Skin Tissue Engineering</strong>."</p> <p><strong><em>Abstract</em></strong><br>Various strategies have extensively explored enhancing the physical and biological properties of chitosan and cellulose scaffolds for skin tissue engineering. This study presents a straightforward method involving the addition of glycerol into highly porous structures of two polysaccharide complexes: chitosan/carboxymethyl cellulose (Chit/CMC) and chitosan/oxidized cellulose (Chit/OC); during a one-step freeze-drying process. Adding glycerol, especially to Chit/CMC, significantly increased stability, prevented degradation, and improved mechanical strength by nearly 50%. Importantly, after 21 days of incubation in enzymatic medium Chit/CMC scaffold has almost completely decomposed, while foams reinforced with glycerol exhibited only 40% mass loss. It is possible due to differences in multivalent cations and polymer chain contraction, resulting in varied hydrogen bonding <br>and, consequently, distinct physicochemical outcomes. Additionally, the scaffolds with glycerol improved the cellular activities resulting in over 40% higher proliferation of fibroblast after 21 days of incubation. It was achieved by imparting water resistance to the highly absorbent material and aiding in achieving a balance between hydrophilic and hydrophobic properties. This study clearly indicates the possible elimination of additional crosslinkers and multiple fabrication steps that can reduce the cost of scaffold production for skin tissue engineering applications while tailoring mechanical strength and degradation.</p> <p><strong>Figure 2.</strong> Morphology. SEM micrographs of the internal structure of the freeze-dried scaffolds. Results of porosity analysis. The methodology and data are described in the README file in the folder.</p> <p><strong>Figure 3.</strong> Mechanical test results. Representative stress-strain curves from the tensile test of all freeze-dried scaffolds, where (A)<br>– measurement performed in dry conditions, (B) – measurement performed in wet conditions. All are described in the README file in the folder.</p> <p><strong>Figure 4. </strong>Swelling behavior of all scaffolds. B – Two representative vials with a visual demonstration of swelling, samples marked with circles: Chit/CMC sample submerged in the PBS (blue circle) and Chit/CMC/Glyc sample floating on the surface (green circle). The arrows lead to photos of scaffolds taken from vials directly after swelling. C – Gel fraction analysis in aqueous solution after 24 <br>6 h. D – Time after which the water droplet is absorbed into the scaffold. E – Photographs of water droplet shape changes on Chit/CMC and Chit/CMC/Glyc scaffolds over time. All are described in the README file in the folder.</p> <p><strong>Figure 5</strong>. Fourier Transform Infrared Spectroscopy (ATR-FTIR) analysis results. Details are in the README file in the folder.</p> <p><strong>Figure 6.</strong> The FTIR spectra of eluates from degraded scaffolds collected on a microscopic glass slide. Details are in the README file in the folder.</p> <p><strong>Figure 7.</strong> The degradation studies of all scaffolds over 21 days of experiments in A – enzymatic medium. B – cell culture medium. Details are in the README file in the folder.</p> <p><strong>Figure 9. </strong>Cell experiments and toxicity analysis. Cytotoxicity of eluates taken from degraded scaffolds. B – Direct fibroblast seeding on scaffolds during 14 days of culture period. C – Direct fibroblast seeding on scaffolds during 14 days of culture period without control to better see the effect of glycerol. Details are in the README file in the folder.</p>
Dataset for the publicaion "Cleaning strategies for 3D-printed porous scaffolds used for bone regeneration fabricated via ceramic vat photopolymerization"
<p>Dataset of publicaion "Cleaning strategies for 3D-printed porous scaffolds used for bone regeneration fabricated via ceramic vat photopolymerization".</p> <p><a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.ceramint.2024.10.160" target="_blank" rel="noreferrer noopener">https://doi.org/10.1016/j.ceramint.2024.10.160</a></p> <p>Dataset includes results of TGA analysis, viscosity measurements and mechnaical properties. </p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.