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Dataset results
266 results for “Protein Modelling”
pLMMoRF: A web server that accurately predicts membrane-interacting molecular recognition features by employing a protein language model
<p>pLMMMoRF predictor scrips and MemMoRF prediction of the human proteome.</p>
Enhanced mTORC1 signaling and protein synthesis in pathologic alpha-synuclein cellular and animal models of Parkinson's disease
<p>Pathologic alpha-synuclein plays an important role in the pathogenesis of alpha-synucleinopathies such as Parkinson's disease (PD). Disruption of proteostasis is thought to be central to pathologic alpha-synuclein (alpha-syn) toxicity; however, the molecular mechanism of this deregulation is poorly understood. Here we report that pathologic alpha-syn activates the mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) leading to enhanced mRNA translation via binding tuberous sclerosis protein (TSC) 2 and destabilizing the TSC1-TSC2 complex. Genetic and pharmacologic inhibition of mTOR and protein synthesis rescue the dopamine neuron loss, behavioral deficits, and aberrant biochemical signaling in the alpha-syn preformed fibril (PFF) and Drosophila alpha-syn transgenic models of pathologic alpha-syn induced degeneration. Our findings establish a potential molecular mechanism by which pathologic alpha-syn activates mTORC1 leading to enhanced protein synthesis and concomitant neurodegeneration in PD.</p>
Simulation data for paper "Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly"
<p>This is the original simulation data sets for paper "Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly".</p>
Data from: Genome-scale annotation of protein binding sites via language model and geometric deep learning
<p>The dataset contains the training and test sets of protein binding sites with DNA, RNA, peptide, protein, ATP, HEM, Zn2+, Ca2+, Mg2+ and Mn2+. Each protein is associated with 3 lines indicating the protein name (PDB accession code and chain), sequence and residue labels (0 for non-binding and 1 for binding), respectively. The ESMFold-predicted structures are also provided.</p>
Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM
<p>This respository corresponds to the following paper: Wankowicz et al. Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM (2024). These are the qFit models. MTZ and deposited models cna be downloaded from the PDB. </p>
Structural models of viral proteins described in Krupovic M, et al., Proc Natl Acad Sci U S A. 2024
<p>This archive contains structural models in PDB format described in Krupovic M, Kuhn JH, Fischer MG, Koonin EV. Natural history of eukaryotic DNA viruses with double jelly-roll major capsid proteins. Proc Natl Acad Sci U S A. 2024</p>
AF2 models for "Co-translational assembly promotes functional diversification of paralogous proteins" by Mallik, et al.
<p>AF2 models used for analyses presented in "Co-translational assembly promotes functional diversification of paralogous proteins" by Saurav Mallik, Angel F. Cisneros, Christian R. Landry, and Emmanuel D. Levy.</p> <p>These models were used to analyze the structural divergence of 3703 Obligatory Homomer, 697 Mixed, and 181 Obligatory Heteromer pairs.</p> <p>Folders are separated into different categories:<br>- Models of homomers (from Schweke et al., 2024. Cell):<br> . AF2_HM_full_models: Full structures of homodimeric models.<br> . AF2_HM_nodiso3: Core structures of homomeric models, trimmed using scripts from Schweke et al. (2023).</p> <p>- Models of heteromers (generated in this work):<br> . AF2_HET_full_models: Full structures of heterodimeric models.<br> . AF2_HET_nodiso3: Core structures of heteromeric models, trimmed using a modified version of the code from Schweke et al. (2023) to work with heterodimers.</p>
Cognition-Associated Protein Structural Changes in a Rat Model of Aging are Related to Reduced Refolding Capacity – Peptide Quantifications
<p>Cognitive decline during aging represents a major societal burden, causing both personal and economic hardship in an increasingly aging population. There are a few well-known proteins that can misfold and aggregate in an age-dependent manner, such as amyloid β and α-synuclein. However, many studies have found that the proteostasis network, which functions to keep proteins properly folded, is impaired with age, suggesting that there may be many more proteins that incur structural alterations with age. Here, we used limited-proteolysis mass spectrometry (LiP-MS), a structural proteomic method, to globally interrogate protein conformational changes in a rat model of cognitive aging. Specifically, we compared soluble hippocampal proteins from aged rats with preserved cognition to those from aged rats with impaired cognition. We identified several hundred proteins as having undergone cognition-associated structural changes (CASCs). We report that CASC proteins are substantially more likely to be nonrefoldable than non-CASC proteins, meaning they typically cannot spontaneously refold to their native conformations after being chemically denatured. The potentially cofounding variable of post-translational modifications is systematically addressed, and we find that oxidation and phosphorylation cannot significantly explain the limited proteolysis signal. These findings suggest that noncovalent, conformational alterations may be general features in cognitive decline, and more broadly, that proteins need not form amyloids for their misfolded states to be relevant to age-related deterioration in cognitive abilities.</p> <p>This deposition provides processed peptide quantifications for all LC-MS/MS proteomics experiments conducted for this study.</p>
Modeling Protein Conformations by Guiding AlphaFold2 with Distance Distributions. Application to Double Electron Electron Resonance (DEER) Spectroscopy.
<p>We describe a modified version of AlphaFold2 that incorporates experiential distance distributions into the network architecture for protein structure prediction. Harnessing the OpenFold platform, we fine-tuned AlphaFold2 on a small number of structurally dissimilar proteins to explicitly model distance distributions between spin labels determined from Double Electron-Electron Resonance (DEER) spectroscopy. We demonstrate the performance of the modified AlphaFold2, referred to as DEERFold, in switching the predicted conformations guided by experimental or simulated distance distributions. Remarkably, the intrinsic performance of AlphaFold2 substantially reduces the number and the accuracy of the widths of the distributions needed to drive conformational selection thereby increasing the experimental throughput. The blueprint of DEERFold can be generalized to other experimental methods where distance constraints can be represented by distributions. </p>
The Effect of Stromal Vascular Fraction (SVF) & Scaffolds Application on Fracture Healing with Bone Defect as Assessed Through Osteocalcin and Bone Morphogenetic Protein-2 (BMP-2) Biomarker Examination: Experimental Study on Murine Model
<p>This data is the raw data for the manuscript with titled The Effect of Stromal Vascular Fraction (SVF) & Scaffolds Application on Fracture Healing with Bone Defect as Assessed Through Osteocalcin and Bone Morphogenetic Protein-2 (BMP-2) Biomarker Examination: Experimental Study on Murine Model.</p>
Data of the protocol paper: Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST
<p>The archived file contains data of the test cases used used in the protocol paper. For each protocol, there's a folder containing input files the protocol takes, and a folder for the protocol output files.</p>
In vivo characterization of antibodies directed against TREAT-AD target proteins in mouse model of AD pathology
<p><em>In vivo </em>characterization of antibodies directed against TREAT-AD target proteins (Moesin, CD44, Midkine, and SFRP1) in the 5xFAD mouse model</p>
Rapid and specific degradation of endogenous proteins in mouse models using auxin-inducible degrons
<p>Auxin-inducible degrons are a chemical genetic tool for targeted protein degradation and are widely used to study protein function in cultured mammalian cells. Here we develop CRISPR-engineered mouse lines that enable rapid and highly specific degradation of tagged endogenous proteins <em>in vivo</em>. Most but not all cell types are competent for degradation. By combining ligand titrations with genetic crosses to generate animals with different allelic combinations, we show that degradation kinetics depend upon the dose of the tagged protein, ligand, and the E3 ligase substrate receptor TIR1. Rapid degradation of condensin I and condensin II – two essential regulators of mitotic chromosome structure - revealed that both complexes are individually required for cell division in precursor lymphocytes, but not in their differentiated peripheral lymphocyte derivatives. This generalisable approach provides unprecedented temporal control over the dose of endogenous proteins in mouse models, with implications for studying essential biological pathways and modeling drug activity in mammalian tissues.</p>
Input files for "Predicting the orientation of adsorbed proteins steered with electric fields using a simple electrostatic model"
<p>In files to run PyGBe (https://github.com/pygbe/pygbe), and reproduce the results from the J. Phys. Chem. B article "Predicting the orientation of adsorbed proteins steered with electric fields using a simple electrostatic model". </p>
Hyperactive antifreeze protein from the beetle Rhagium mordax stabilizes model lipid membranes during temperature dependent phase transition
<p>Data from the study submitted in the paper Hyperactive antifreeze protein from the beetle Rhagium mordax stabilises model lipid membranes during temperature-dependent phase transition</p> <p>Data Includes;</p> <p>1. DSC results of RmAFPs interactions with liposomes showing Tm, ΔHcal and Full width at half maximum (FWHM) as well as Phase transitions thermographs by DSC on 1.5mg/ml SUV liposomes either with 60μM (or 0.75mg/ml) RmAFPs or without RmAFPs as control.</p> <p>2. fluorescence spectroscopy data, a complete compilation</p>
Multimodal dataset: Protein Function Prediction using STRING data & COVID19 Mortality Model by EI
<p>The PFP.zip file contains 1. 5 well-formated GO terms dataset for EI, 2. STRING data 3. GO term annotation. The last two could be merged by the 'generate_data.py' script in https://github.com/GauravPandeyLab/ensemble_integration</p> <p>The covid19_model_built.zip contained the EI model built based on the COVID-19 Mortality dataset, the detail of usage are here:.</p>
Mining Proteomic Databases of a Model Plant Medicago truncatula for Mosaic Proteins and Other Unconventional Translation Products
<p><strong>How many different proteins can be produced from a single spliced transcript? Genome annotation projects do not consider the coding potential of reading frames other than that of the reference open reading frames (refORFs). Recently, alternative open reading frames (altORFs) and their translational products, alternative proteins (altProts), have been shown to carry out important functions in various organisms. Overlapping altORFs may be involved in one fundamental mechanism so far overlooked. A few years ago, it was proposed that altORFs may act as building blocks for chimeric (mosaic) polypeptides, which are produced via multiple ribosomal frameshifting events from a single mature transcript. We adopt terminology from that earlier discussion and call this mechanism mosaic translation. This way of extracting and combining genetic information may significantly increase proteome diversity. Thus, we hypothesize that this mechanism may have contributed to the flexibility and adaptability of organisms to a variety of environmental conditions. The idea of mosaic translation is a testable hypothesis, although its direct demonstration is technically very challenging. If confirmed, this concept will revolutionize modern genetics. In this project, we would like to follow a unique strategy for the detection of mosaic proteins in proteomic databases publicly available for a very important model plant <em>Medicago truncatula</em>. The proposed analysis will be based on our own preliminary data already generated in the course of an ongoing TÜBİTAK1002 project. Regardless of whether the evidence for mosaic translation is found in this study, this effort will help identify such proteins later when more proteomic data become available. Finally, our approach can reveal unconventional frameshifting products that derive from the omission of several nucleotides by ribosomes (for example, +2 to +16 frameshifts). Regardless of whether such frameshifted products are parts of mosaic proteins, the potential for their detection makes this project very novel, because frameshifts longer than one nucleotide in the forward direction have not been described so far.</strong></p>
Project files provided as supporting information to the manuscript "Fast, accurate, and system-specific variable-resolution modelling of proteins"
<p>Project files provided as supporting information to the manuscript "Fast, accurate, and system-specific variable-resolution modelling of proteins".</p> <p>The dataset contains the following files:</p> <p>- RMSD_adk: files containing the root-mean-square deviation computed on the C-alpha atoms/beads in the atomistic and CANVAS simulations of adk (Figure 6).</p> <p>- RMSF_adk: files containing the root-mean-square fluctuations of the C-alpha atoms/beads in the atomistic and CANVAS simulations of adk (Figure 6).</p> <p>- APBS_adk: PQR file of the system and DX file of the surface potential, for both the atomistic and CANVAS systems (Figure 7).</p> <p>- SASA_antibody: files containing the per-residue solvent accessible surface area of the atomistic region of the ake protein, in the atomistic and CANVAS simulations (Figure 8).</p> <p>- RMSF_antibody: files containing the root-mean-square fluctuations of the C-alpha atoms/beads in the atomistic and CANVAS simulations of antibody (Figure 9).</p> <p>- APBS_antibody: PQR file of the system and DX file of the surface potential, for both the atomistic and CANVAS systems (Figure 10).</p> <p>- SASA_antibody: files containing the per-residue solvent accessible surface area of the hinge region of the antibody for each conformational cluster, in the atomistic and CANVAS simulations (Figure 11).</p> <p>- RMSIP_antibody: RMSIP between the essential subspaces computed from the atomistic and CANVAS simulations (Figure S3).</p> <p>- rgyr_antibody: files containing the radii of gyration of the antibody for each conformational cluster, in the atomistic and CANVAS simulations (Figure S4).</p> <p>- ake_AA.mp4: video of the all-atom simulation of adenylate kinase</p> <p>- ake_canvas.mp4: video of the canvas simulation of adenylate kinase</p>
Data table 5 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)
<div>An Excel table contains a list of proteins identified by MS from pull-down experiment using cerebellar cortex lysates with Dynabeads coated with anti-ataxin-3 1H9 mouse monoclonal antibodies. The false positive interactor proteins were excluded from this list by subtracting proteins found in "Supplementary_table 2_cortex isogenic mouse IgG control dynabeads.xlsx" </div> <div> </div>
Data table 4 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)
<div>An Excel table contains a list of proteins identified by MS from a pull-down experiment using cerebellum lysates with Dynabeads coated with anti-ataxin-3 1H9 mouse monoclonal antibodies. The false positive interactor proteins were excluded from this list by subtracting proteins found in "Supplementary_table 3_cerebellum isogenic mouse IgG control dynabeads.xlsx<span><br></span></div>
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.