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3,878 results for “Molecular Data”
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (D59Y) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (D59Y).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (E76G) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (E76G).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of rat phenylalanine hydroxylase (rPAH) tetramer
<p>Raw data of molecular dynamics simulations of rat phenylalanine hydroxylase (T22-K450) tetramer. Missing residues were rebuilt using Modeller. Metal site was parameterized using MCPB.py in AmberTools. Simulation starts from the crystal pose (PDB: 5DEN).</p>
Molecular dynamics simulation data of rat phenylalanine hydroxylase (rPAH) monomer
<p>Raw data of molecular dynamics simulations of rat phenylalanine hydroxylase (T22-K450) monomer. Missing residues were rebuilt using Modeller. Metal site was parameterized using MCPB.py in AmberTools. Simulation starts from the crystal pose (PDB: 5DEN).</p>
Molecular dynamics simulation data of regulatory ACT domain monomer mutation (T63P) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain monomer mutation (T63P). Simulation setup files are also included. 21 starting conformations are used in simulations. </p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (R68S) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (R68S).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (T63P) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (T63P).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (L48S) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (L48S).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (K42I) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (K42I).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (I65T) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (I65T).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (I65S) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (I65S).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Supplementary molecular docking and dynamics data of poxin inhibitors of mpox
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This record contains raw data related to the article "Sex-Specific Cell Types and Molecular Pathways Indicate Fibro-Calcific Aortic Valve Stenosis"
<p>This record contains raw data related to the article "Sex-Specific Cell Types and Molecular Pathways Indicate Fibro-Calcific Aortic Valve Stenosis"</p> <p><strong>Background:</strong> Aortic stenosis (AS) is the most common valve disorder characterized by fibro-calcific remodeling of leaflets. Recent evidence indicated that there is a sex-related difference in AS development and progression. Fibrotic remodeling is peculiar in women’s aortic valves, while men’s leaflets are more calcified. Our study aimed to assess aortic valve fibrosis (AVF) in a severe AS cohort using non-invasive diagnostic tools and determine whether sex-specific pathological pathways and cell types are associated with severe AS.</p> <p><strong>Materials and Methods:</strong> We have included 28 men and 28 women matched for age with severe AS who underwent echocardiography and cardiac contrast-enhanced computed tomography (CT) before intervention. The calcium and fibrosis volumes were assessed and quantified using the ImageJ thresholding method, indexed calcium and fibrosis volume were calculated by dividing the volume by the aortic annular area. For a deeper understanding of molecular mechanisms characterizing AS disorder, differentially expressed genes and functional inferences between women and men’s aortic valves were carried out on a publicly available microarray-based gene expression dataset (GSE102249). Cell types enrichment analysis in stenotic aortic valve tissues was used to reconstruct the sex-specific cellular composition of stenotic aortic valves.</p> <p><strong>Results:</strong> In agreement with the literature, our CT quantifications showed that women had significantly lower aortic valve calcium content compared to men, while fibrotic tissue composition was significantly higher in women than men. The expression profiles of human stenotic aortic valves confirm sex-dependent processes. Pro-fibrotic processes were prevalent in women, while pro-inflammatory ones, linked to the immune response system, were enhanced in men. Cell-type enrichment analysis showed that mesenchymal cells were over-represented in AS valves of women, whereas signatures for monocytes, macrophages, T and B cells were enriched men ones.</p> <p><strong>Conclusions:</strong> Our data provide the basis that the fibro-calcific process of the aortic valve is sex-specific, both at gene expression and cell type level. The quantification of aortic valve fibrosis by CT could make it possible to perform population-based studies and non-invasive assessment of novel therapies to reduce or halt sex-related calcific aortic valve stenosis (CAVS) progression, acting in an optimal window of opportunity early in the course of the disease.</p>
Data for the manuscript "Identification and structural studies of the crucial RNAi target of SARS-CoV-2 through molecular dynamics simulations"
<p>Simulation datasets for manuscript titled "<strong>Identification and structural studies of the crucial RNAi target of SARS-CoV-2 through molecular dynamics simulations"</strong></p>
DNA Methylation Data-based Molecular Subtype Classification Related to the Prognosis in Patients with esophageal carcinoma
<p>Supplemental Materials of the manuscript named "DNA Methylation Data-based Molecular Subtype Classification Related to the Prognosis in Patients with esophageal carcinoma",which have been submitted to the journal <em>international journal of molecular sciences</em></p>
Dataset raw data related to article "In-depth genetic and molecular characterization of Diaphanous Related Formin 2 (DIAPH2) and its role in the inner ear"
<p>This record contains the raw data (Exome sequencing) related to article "In-depth genetic and molecular characterization of DIAPH2 as a novel candidate gene for hearing loss"</p> <p><strong>ABSTRACT </strong></p> <p>Hereditary hearing loss is characterized by an extreme genetic heterogeneity. Nowadays, whole-exome sequencing represents a reasonably cost-effective approach for both mutational screening of known deafness genes and novel disease-gene identification. Here, we investigate the role of Diaphanous-related formin 2 (DIAPH2), coding for a protein involved in actin filament elongation, in nonsyndromic hearing loss. Using whole-exome sequencing, we found a predicted pathogenic missense variant at a conserved site in <em>DIAPH2</em>, which segregated with nonsyndromic X-linked hearing loss in an Italian family. Our immunohistochemical studies indicated that the mouse ortholog protein Diaph2 is expressed during development in the cochlea, specifically in the actin-rich stereocilia of the sensory outer hair cells. <em>In-vitro</em> studies showed a possible functional impairment of the mutant DIAPH2 protein upon RhoA-dependent activation. Finally, <em>Diaph2</em> knock-out and knock-in mice were generated by CRISPR/Cas9 technology and auditory brainstem response measurements performed at 4, 8 and 14 weeks. However, no hearing impairment was detected, possibly due to functional redundancy/compensation by other diaphanous proteins. Our findings indicate that <em>DIAPH2</em> may play a role in the inner ear; further studies are however needed to clarify the contribution of <em>DIAPH2</em> to deafness.</p> <p> </p>
The molecular raw data of microbial communities associated with fish gut - in vitro model system using 16S rRNA Illumina amplicon sequencing approach.
<p>This data on the microbial communities and its diversity associated with fish gut. The samples were obtained from fish gut - in vitro model system using 16S rRNA Illumina amplicon sequencing approach.</p>
The molecular raw data of microbial communities associated with fish gut
<p>This data on the microbial communities and its diversity associated with fish gut.</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.