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Dataset results
295 results for “Structure prediction”
Structure prediction analysis of huntingtin using Phyre2 (2016/03/07)
<p>Huntingtin structure-function open lab notebook project</p>
RaptorX structure prediction of huntingtin
<p>Huntingtin structure-function open lab notebook project. </p>
PfamSDB, The structural database of Pfam seeds made by cutting the Full-Length Alphafold predicted structures
<p>PfamSDB.tar contains the gzipped pdb file of Pfam seeds.</p><p>PfamSDB_cutFS.tar.gz contains the Foldseek database of Pfam seeds made by cutting the database of Full-length proteins.</p>
Data and structures for "How accurately can we predict binding poses with AlphaFold models?
<p>Contains structures generated by AlphaFold, models from GPCRdb, and structures of proteins from PDB. </p> <p>Additionally computed rmsds for pockets, backbone, and poses, and scripts to create figures.</p> <p> </p> <p> </p>
DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model.
<p>test and training data.</p>
Geographic drivers more important than landscape composition in predicting bee beta diversity and community structure
<p>The importance of microhabitat traits such as floral availability is well known; however, forest bee spatial dynamics have been variably studied across local to broad geographic scales. Past literature suggests that landscape factors from proximate to distal are important in determining forest bee community metrics, including richness, abundance, and taxonomic composition. Leveraging the interest and assistance of citizen science volunteers, we employed standard bee bowl trap transects across Maryland, Delaware, northern Virginia, and the District of Columbia and identified correlations between bee community composition, local and regional landcover, and broader geospatial patterns. We also identified the partial contributions of both specific species and sampling sites to total beta diversity. Various landcover metrics were significantly related to bee community structure, with bee abundance positively and negatively correlated with forest and wetland cover, respectively. In general, land cover metrics within a 1,000-m buffer exhibited stronger correlations with bee communities; however, broader geographic variation, using Cartesian coordinates north and east as indices, was most significantly correlated with the bee community. Specifically, bee communities were less rich to the east and south of the study area. We also identified similar correlations with the bee community as categorized both by trophic and nesting behaviors, with both geographic northing and easting proving to be most strongly correlated with the forest bee community. Results of beta diversity and cluster analyses showed that the most species-depauperate sites exhibited the highest contributions to beta diversity and that species-poor sites consisted of a reduced subset of the greater community. Our results show that successful bee conservation must consider, beyond local-scale resource availability, broad geospatial considerations and forest habitat connectivity across political and administrative boundaries.</p>
Antibody-Antigen Models for McCoy 2024 Paper: "A Comparison of Antibody-Antigen Complex Sequence-to-Structure Prediction Methods and their Systematic Biases"
<p>Up to the top 20 models generated for each method tested in the 2024 Paper: "A Comparison of Antibody-Antigen Complex Sequence-to-Structure Prediction Methods and their Systematic Biases"</p>
Source data for manuscript(De novo protein design with a denoising diffusion network independent of pre-trained structure prediction models)
<p>This respository contains the source data for figure and supplementary figure in manuscript(SCUBA-D).</p>
Source data for manuscript(De novo protein design with a denoising diffusion network independent of pre-trained structure prediction models)
<p>This respository contains the source data for figure and supplementary figure in manuscript(SCUBA-D).</p>
predicted_protein_complex_structures_datasets
Open the record for dataset details and reuse information.
Screening of 6000 compounds for uncoupling activity: input parameters, the predicted uncoupling activity, as well as the results in respect to structural alerts
<p>Protonophoric uncoupling of phosphorylation is an important factor when assessing chemicals for their toxicity, and has recently moved into focus in pharmaceutical research with respect to the treatment of diseases such as cancer, diabetes or obesity. Reliably identifying uncoupling activity is thus a valuable goal. To that end, we screened more than 6000 anionic compounds for in-vitro uncoupling activity, using a biophysical model based on ab-initio COSMO-RS input parameters with the molecular structure as the only external input. We combined these results with a model for baseline toxicity (narcosis). Our model identified more than 1250 possible uncouplers in the screening dataset, and identified possible new uncoupler classes such as thiophosphoric acids. When tested against 423 known uncouplers and 612 known inactive compounds in the dataset, the model reached a sensitivity of 83% and a specificity of 96%. In a direct comparison, it showed a similar specificity than the structural alert profiler Mitotox (97%), but much higher sensitivity than Mitotox (47%). The biophysical model thus allows for a more accurate screening for uncoupling activity than existing structural alert profilers. We propose to use our model as a complementary tool to screen large datasets for protonophoric uncoupling activity in drug development and toxicity assessment.</p>
Neutrophil-mediated oxidative stress and albumin structural damage predict COVID-19-associated mortality
<p>This work reports that COVID-19-induced oxidative stress inflicts structural damages to human serum albumin (HSA) and is linked with mortality outcome in critically ill patients. Analyzing blood samples from patients and healthy individuals, the paper provides evidence that neutrophils are major sources of oxidative stress in blood and that hydrogen peroxide is highly accumulated in plasmas of non-survivors. The electron paramagnetic resonance spectra of spin-labeled fatty acids (SLFAs) bound with HSA in whole blood of control, survivor, and non-survivor subjects (n=10–11) were analyzed to probe structural damages to the protein. Non-survivors' HSA showed dramatically altered biophysical parameters that reflect remarkably fluid protein microenvironments. Following loading/unloading of 16-DSA, the results show that the transport function of HSA may be impaired in severe patients. Stratified at the means, Kaplan–Meier survival analysis indicated that lower values of S/W ratio and accumulated H<sub>2</sub>O<sub>2</sub> in plasma significantly predicted in-hospital mortality.</p>
Data for: Biogeographic history predicts bee community structure across floral resource gradients in southeast Australia
<p><strong><span>Aim:</span></strong><span> Plants populations are declining in their native ranges around the globe through the expansion of agriculture, urbanization, and plant invasions. We test the hypothesis that animal species that have spent more of their evolutionary history in a region are more dependent on native plants, particularly those plants that have spent more of their evolutionary history in the region, and are therefore more negatively impacted by native plant decline. </span></p> <p><strong><span>Location:</span></strong><span><strong> </strong>Yarra Valley landscapes, Australia</span></p> <p><strong><span>Methods</span></strong><span><strong>:</strong> We test the presence and pattern of phylogenetic signal in native bee community responses to local flower density of ancient Australian plant lineages and the amount of native vegetation in the surrounding landscape across farm and native vegetation sites. We also test phylogenetic signal in the frequency of bee visitation to flowers from ancient Australian plant lineages. We compare the patterns of phylogenetic signal to the current understanding of bee biogeographic histories to evaluate our hypothesis. </span></p> <p><strong><span>Results:</span></strong><span> There was significant phylogenetic signal in responses to flower density of plants from ancient Australian lineages, and the frequency of visitation to these flowers, with most species from the ancient Australian bee clade being positively associated with these flowers. This is consistent with our hypothesis. Significant phylogenetic signal in response to native vegetation in the surrounding landscape was driven primarily by the more recently arrived bee linages, with ancient lineages able to persist on some farms where ancient Australian flowers were present (e.g. on roadsides). </span></p> <p><strong><span>Main conclusions:</span></strong><span> Bee species that have spent more of their evolutionary history in Australia are more dependent on ancient Australian plant lineages and so most negatively impacted by the decline of these plants. This may be a broader phenomenon because phylogenetic conservatism in host plant use, the main assumption underlying our hypothesis, is common among herbivorous arthropods (~500,000 species).</span></p>
Cell Anomaly Localisation using Structured Uncertainty Prediction Networks
<p>Fluorescent and brightfield datasets for "Cell Anomaly Localisation using Structured Uncertainty Prediction Networks", part of MIDL 2022.</p>
Prediction of ternary complex structures using molecular dynamics and proteomics
<p>Source code and structural PDBs that went into the Prediction of ternary complex structures using molecular dynamics and proteomics paper.</p>
Raw data for 'Prediction of Photodynamics of 200 nm Excited Cyclobutanone with Linear Response Electronic Structure and Ab Initio Multiple Spawning'
<p>Raw data from AIMS simulations and scripts for image generation for the paper "Prediction of Photodynamics of 200 nm Excited Cyclobutanone with Linear Response Electronic Structure and Ab Initio Multiple Spawning": J. Chem. Phys. 2024.</p>
Raw data for "Ancestral structure prediction reveals the conformational impact of the RuBisCO small subunit across time".
<p>The repository contains raw data for the article "Ancestral structure prediction reveals the conformational impact of the RuBisCO small subunit across time".</p> <p>The repository contains:</p> <ol> <li>Dataset for the RbcL and RbcS sequences along with the inferred sequences for the ancestors of interest</li> <li>Phylogenetic tree for the concatenated and separate RbcL-RbcS sequences.</li> <li>Structures for the extant and ancestral RuBisCO complexes used in the study.</li> <li>Solvated pdb files for creating the topology files required for MD-simulations.</li> </ol>
AlphaFold2 predicted structures of ThsA and ThsB proteins
<p>This Zenodo record contains the AlphaFold2 models described in the manuscript: Structural characterization of macro domain-containing Thoeris antiphage defense systems</p>
Source data of Mirtronstructdb - A comprehensive database of mirtrons with predicted secondary structure
Open the record for dataset details and reuse information.
FIGURE 2. Predicted secondary structures for 22 in The complete mitochondrial genome of the jumping grasshopper Sinopodisma pieli (Orthoptera: Acrididae) and the phylogenetic analysis of Melanoplinae
FIGURE 2. Predicted secondary structures for 22 tRNA genes of the S. pieli mitogenome. The tRNAs are labeled with the abbreviations of their corresponding amino acids. The minus sign (-) indicates Watson-Crick base pairing and plus sign (.) indicates G-U base pairing.
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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.