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650 results for “molecular mechanisms”
Histological and Molecular Mechanisms of Pain in Patient With Chronic Pain From Adhesions
ClinicalTrials.gov study NCT03938168. IPD Sharing: YES. Countries: 1. Publications: 5.
Untangling the structural and molecular mechanisms underlying colour and rapid colour change in a lizard, Agama atra
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Parallel molecular mechanisms for enzyme temperature adaptation
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Data from: Molecular mechanisms of postmating prezygotic reproductive isolation uncovered by transcriptome analysis
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Transcriptomics Reveal Specific Molecular Mechanisms Underlying Transgenerational Immunity in Manduca sexta
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Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation
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Data for "Molecular mechanism of biased signaling in a prototypical G protein–coupled receptor"
<p>Data and analysis code for "Molecular mechanism of biased signaling in a prototypical G protein–coupled receptor" (Suomivuori <em>et al.</em>, Science 367, 881–887 (2020)). See the included READMEs for more details. Please cite the paper if you use these data.</p>
Raw data related to: Molecular Mechanisms Controlling Foxp3 Expression in Health and Autoimmunity: From Epigenetic to Post-translational Regulation.
<p><strong>Abstract</strong></p> <p>The discovery of the transcription factor Forkhead box-p3 (Foxp3) has shed fundamental insights into the understanding of the molecular determinants leading to generation and maintenance of T regulatory (Treg) cells, a cell population with a key immunoregulatory role. Work over the past few years has shown that fine-tuned transcriptional and epigenetic events are required to ensure stable expression of Foxp3 in Treg cells. The equilibrium between phenotypic plasticity and stability of Treg cells is controlled at the molecular level by networks of transcription factors that bind regulatory sequences, such as enhancers and promoters, to regulate Foxp3 expression. Recent reports have suggested that specific modifications of DNA and histones are required for the establishment of the chromatin structure in conventional CD4+ T (Tconv) cells for their future differentiation into the Treg cell lineage. In this review, we discuss the molecular events that control Foxp3 gene expression and address the associated alterations observed in human diseases. Also, we explore how Foxp3 influences the gene expression programs in Treg cells and how unique properties of Treg cell subsets are defined by other transcription factors.</p> <p> </p> <p><strong>Progetto giovani ricercatori</strong>[GR-2016-02363725] dal titolo: "Immune Tolerance, Metabolism and Multiple Sclerosis: Novel Molecular Tools to Monitor Disease Pathogenesis and Progression"</p> <p> </p> <p> </p> <p> </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>
Structuran and NMR Characterization of Hexamer and Octamer Foldamers in Chloroform and Water: A Molecular Dynamics and Quantum Mechanics Approach
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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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Inference of molecular mechanisms of transcriptional regulation from co-expression data
<p>The accompanying data for the article "Inference of molecular mechanisms of transcriptional regulation from co-expression data". The article is now live on Research Square <a href="https://doi.org/10.21203/rs.3.rs-1262163/v1">10.21203/rs.3.rs-1262163/v1</a></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>
Transcriptome analysis reveals potential molecular mechanisms underlying differences in stalk color among four Gastrodia elata varieties-Supplementary Material
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Data for "Proteome-wide prediction of mode of inheritance and molecular mechanism underlying genetic diseases using structural interactomics"
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Data for "The Molecular Mechanism of Light-induced Bond Formation and Breakage in the Cyanobacteriochrome TePixJ"
<p>Data used to generate the figures in the publication "The Molecular Mechanism of Light-induced Bond Formation and Breakage in the Cyanobacteriochrome TePixJ".</p>
Fig. 2 in Astragalus species: Phytochemistry, biological actions and molecular mechanisms underlying their potential neuroprotective effects on neurological diseases
Fig. 2. Chemical structure of Astragalus polysaccharide (Liu et al., 2020).
Fig. 4 in Astragalus species: Phytochemistry, biological actions and molecular mechanisms underlying their potential neuroprotective effects on neurological diseases
Fig. 4. Astragalus spinosus (Alsirhan, 2002).
Molecular mechanisms of regulation by a β-alanine-responsive Lrp-type transcription factor from Acidianus hospitalis
<p>This dataset contains the raw data that lie at the basis of the results discussed in <strong>Chapter 5: Molecular mechanisms of regulation by a β-alanine-responsive Lrp-type transcription factor from Acidianus hospitalis </strong>of the PhD thesis of Amber Bernauw. This chapter is also published as an article at MicrobiologyOpen (<a href="https://doi.org/10.1002/mbo3.1356">https://doi.org/10.1002/mbo3.1356</a>).</p>
(Botox) Mechanisms of Action in Altering the Molecular Environment in Which Pain Fibers Exist
ClinicalTrials.gov study NCT03381261. IPD Sharing: NO. Countries: 1. Publications: 0.
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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.