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266 results for “Protein Modelling”
Supplemental Material for 'Deep Generative Models of Protein Structure Uncover Distant Relationships Across a Continuous Fold Space' and DeepUrfold
<p>Data provided for the paper Draizen, EJ, Veretnik, S, Mura, C, and Bourne, PE. "Deep Generative Models of Protein Structure Uncover Distant Relationships Across a Continuous Fold Space." <em>Nature Communications</em>, Aug. 2024.</p> <div> </div> <p> </p>
Predicting the pro-longevity or anti-longevity effect of model organism genes with enhanced Gaussian noise augmentation-based contrastive learning on protein-protein interaction networks
<p>The datasets used to evaluate Enhanced Gaussian noise augmentation-based contrastive learning (EGsCL) against predicting the pro-longevity or anti-longevity effect of model organism gene. This repo also includes the pretrained encoders that obtained the best predictive performance for each organism (see Table 2).</p>
Data table 3 from publication "Impaired interactions of ataxin-3 with protein complexes reveals their specific structure and functions in SCA3 Ki150 model" (doi.org/10.3389/fnmol.2023.1122308)
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ProteinInvBench: Benchmarking Protein Design on Diverse Tasks, Models, and Metrics
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Micro-anatomic alterations of the placenta in a non-human primate model of gestational protein-restriction
<p><span><span><span><span><span><span><span><span><span><span><span><u>Objectives:</u> Maternal protein malnutrition is associated with impaired fetal growth, and lifetime consequences for the offspring. Our group has previously developed a model of protein-restriction in the non-human primate, which was associated with fetal growth restriction, stillbirth, decreased placental perfusion, and evidence of fetal hypoxia, suggesting perturbed vascular development. Previous assessments of placental vasculature have relied upon stereological or vascular casting methods, but these methods have limitations. Our objective was to histologically characterize the micro-anatomic alterations associated with adverse pregnancy outcomes using a newer method that permits investigation of the 3D vascular structure and surrounding histology.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><u>Methods:</u> Rhesus macaques were assigned in the pre-gestational period to a control diet that contained 26% protein, or study diet containing 13% protein (50% PR diet). Placental tissue was collected at delivery and processed using a clarification, immunohistochemistry, and confocal microscopy protocol published previously by our group. 3-dimensional reconstructions and quantitative analysis of the vascular micro-anatomy was performed using analysis software (Imaris®) and statistical analysis incorporated maternal, pregnancy, and perinatal outcomes.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><u>Results:</u> In unadjusted analysis, when comparing those pregnancies on a 50% PR diet (n=4) with those on a control diet (n=4), protein-restriction diet was associated with decreased maternal pre-pregnancy weight (difference of -1.975kg, 95% CI -3.267 to -0.6826). When controlling for maternal pre-pregnancy weight, fetal sex, and latency from tissue collection to imaging, a gestational protein-restriction diet was associated with decreases in total vascular length, total vascular surface area, total vascular volume, and vascular density.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><u>Conclusion:</u> In this pilot study, a gestational protein-restriction diet was associated with changes in the placental micro-vasculature, which may be related to the observed adverse pregnancy outcomes and perturbed placental perfusion demonstrated in this model.</span></span></span></span></span></span></span></span></span></span></span></p>
Native protein of HP model
<p>A collection and formated dataset of designable (g=1) HP sequence and conformation. Generated by software of Anders Irbäck and Carl Troein (Enumerating designing sequences in the HP model, <em>Journal of Biological Physics</em> <strong>28</strong>, 1-15, 2002).</p>
The dataset used in "A max-margin model for predicting residue-base contacts in protein-RNA interactions"
<p>The dataset used in "A max-margin model for predicting residue-base contacts in protein-RNA interactions"</p>
Data set for "The effects of glycine to alanine mutations on the struc-ture of GPO collagen model proteins"
<p>Data set for "The effects of glycine to alanine mutations on the struc-ture of GPO collagen model proteins"</p> <p>The README files contain a description of all files and scripts in this repo.</p>
Model files for "Modeling Protein-Nucleic Acid Complexes with Extremely Large Conformational Changes using Flex-LZerD"
<p>Models in PDB format generated for "Modeling Protein-Nucleic Acid Complexes with Extremely Large Conformational Changes using Flex-LZerD" by domain-based docking and flexible fitting. See summary Table 2.</p>
Conformational ensembles used in "Assessment of forward models for the hydrodynamic radius of intrinsically disordered proteins. Pesce et al. 2022"
<p>Ensemble of intrinsically disordered proteins used in: <em>"Assessment of forward models for the hydrodynamic radius of intrinsically disordered proteins. Pesce et al. 2022"</em>.</p> <p>Ensembles are produced with Flexible-meccano and Langevin simulations with CALVADOS for:</p> <ul> <li>Hst5</li> <li>RS</li> <li>DSS1</li> <li>Sic1</li> <li>ProTa</li> <li>NHE6cmdd</li> <li>A1</li> <li>aSyn</li> <li>ANAC046</li> <li>GHR-ICD</li> <li>Tau</li> </ul>
Data-specific substitution models improve protein-based phylogenetics - data
<p>Amino-acid sequence data sets, estimated data-specific amino-acid substitution models, and optimal ML trees.</p> <p>Data are divided in five folders, each one with a readme.txt file describing it.</p> <p>├── 1_simulated_data_sets<br> │ ├── 1500-site_alignments<br> │ ├── 400-site_alignments<br> │ └── 8000-site_alignments<br> ├── 2_simulated_data_specific_models<br> │ ├── Codeml_models<br> │ ├── FastMG_models<br> │ ├── IQTREE_models<br> │ ├── P4_BI_models<br> │ └── P4_ML_models<br> ├── 3_optimal_ML_trees_simulated_data<br> │ ├── commonly-used_empirical_models<br> │ │ ├── cpREV_model_analyses<br> │ │ └── WAG_model_analyses<br> │ ├── data_specfic_model_analyses<br> │ │ ├── Codeml-estimated_model_analyses<br> │ │ ├── FastMG-estimated_model_analyses<br> │ │ ├── IQTREE-estimated_model_analyses<br> │ │ ├── P4BI-estimated_model_analyses<br> │ │ └── P4ML-estimated_model_analyses<br> │ └── simulation_model_analyses<br> ├── 4_data_specific_models_empirical_data<br> │ └── Toussaint18_data_specific_models_27partitions<br> └── 5_optimal_ML_trees_empirical_data</p>
Case studies from: Sequence assignment validation in protein crystal structure models with checkMySequence
<p>Case studies from "Sequence assignment validation in protein crystal structure models with checkMySequence"</p>
Enhancing Protein Sequence Annotation in Viral Genomics Using Large Language Models and Soft Alignments.
<p>List of 200 most abundant VOG descriptions.</p>
Protein sequences matching TIGRFAM models
<p>A set of 411 large and 3,001 small TIGRFAM protein families originally used for benchmarking sequence clustering programs. Large families contain at least 20,000 sequences with a genus label, whereas small contain fewer than 20,000. Sequences were downloaded from <a href="https://www.ncbi.nlm.nih.gov/genome/annotation_prok/tigrfams/">NCBI</a> and renamed by their original name (accession number) followed by their semi-colon separated NCBI taxonomy of the originating organism. For example, the first sequence in TIGRFAM_large/TIGRFAM00005.fas.gz is named:</p><blockquote><p>WP_000005837.1 RluA family pseudouridine synthase, partial [Bacillus anthracis];TIGR00005(group);cellular organisms(no rank);Bacteria(superkingdom);Terrabacteria group(clade);Firmicutes(phylum);Bacilli(class);Bacillales(order);Bacillaceae(family);Bacillus(genus);Bacillus cereus group(species group);Bacillus anthracis(species)</p></blockquote>
iDentification and vAlidation Model of Liquid biopsY Based cfDNA Methylation and pRotEin biomArKers for Pancreatic Cancer (DAYBREAK Study)
ClinicalTrials.gov study NCT05495685. IPD Sharing: NO. Countries: 1. Publications: 49.
Modelling the Interaction Between Rationally-designed Synthetic Model Viral Protein Immunogens
ClinicalTrials.gov study NCT03816137. IPD Sharing: YES. Countries: 1. Publications: 1.
Development of Inflammatory Disease Model Protein, Genetic and Microbial Biomarkers
ClinicalTrials.gov study NCT00980525. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Data from: Cost of reproduction in the Queensland fruit fly: Y-model vs. lethal protein hypothesis
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Data from: Oncogene inference optimization using constraint-based modelling incorporated with protein expression in normal and tumour tissues
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Serum levels of tau protein increase according to the severity of the injury in DAI rat model
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ScienceDex guides
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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.