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73 results for “structural disorder”
Datasets of sequences, alignments and structural models generated for the structural prediction of complexes mediated by intrinsically disordered regions.
<p>This repository contains input and ouput files used and generated for the scanning of intrinsically disordered region and the prediction of their binding sites to receptor proteins using the <a href="https://github.com/i2bc/SCAN_IDR">SCAN_IDR</a> pipeline with AlphaFold2-Multimer.</p><p>It contains two archives: </p><ol><li><a href="https://zenodo.org/api/records/10068949/draft/files/scanidr_data_repository_corr6J08.tar/content"><i><strong>scanidr_data_repository_corr6J08.tar</strong></i></a> dedicated to the analysis of a dataset of 42 protein complexes non redundant with the dataset used for AlphaFold2 training,</li><li><a href="https://zenodo.org/api/records/10068949/draft/files/923_elm_cases_repository.tar.gz/content"><i><strong>923_elm_cases_repository.tar.gz</strong></i></a> dedicated to the analysis of 923 complexes from the ELM database.</li></ol><p>These data can be used to rerun specific sections of the pipeline and scripts provided in: <a href="https://github.com/i2bc/SCAN_IDR">https://github.com/i2bc/SCAN_IDR</a></p><h4><strong>Dataset of 42 non redundant complexes</strong></h4><p>The first archive <a href="https://zenodo.org/api/records/10068949/draft/files/scanidr_data_repository_corr6J08.tar/content"><i><strong>scanidr_data_repository_corr6J08.tar</strong></i></a> contains 3 compressed directories and a README file detailing their contents :</p><ul><li>the initial raw sequence and alignment data for every chain -> DIRECTORY <strong>fasta_msa/</strong></li><li>the input and output data of every Alphafold run for every complex -> DIRECTORY <strong>af2_runs/</strong></li><li>the native reference structures -> DIRECTORY <strong>ref_capri_curated/</strong></li></ul><p>The protein-peptide complex cases have been assigned a distinct index number, from 1 to 42, consistent across the several directories of the archive. Their corresponding directories are labelled as <i><index>_<pdbcode></i>.</p><p><i>The models in this archive were generated using AlphaFold2-Multimer v2.2</i></p><h4><strong>Dataset of 923 complexes selected from the ELM database</strong></h4><p>The second archive <a href="https://zenodo.org/api/records/10068949/draft/files/923_elm_cases_repository.tar.gz/content"><i><strong>923_elm_cases_repository.tar.gz</strong></i></a> contains input and ouput files used and generated for the analysis of 923 Eukaryotic Linear Motifs (ELM) database entries.</p><p>Each ELM entry is indexed with specific integer id and is composed of a receptor and a ligand protein. </p><p>The archive contains a Table associating ELM indexes with the ELM entry information, 5 directories and a README file detailing their contents:</p><ul><li>the table describing ELM entries -> FILE <strong>Table_923ELM_uid_delimitations_info_for_archive.txt</strong></li><li>the initial raw sequence and multiple sequence alignment (MSA) data for every chain -> DIRECTORY <strong>fasta_msa/</strong></li><li>the concatenated MSA model for every ELM complex and protocol used -> DIRECTORY <strong>af2_elm_coali_inputs/</strong></li><li>the best model of every AF2 protocol for every complex according to the AF2 -> DIRECTORY <strong>af2_elm_models/</strong></li><li>the best model cut in the ligand part to select only the ELM motifs as used for the evaluation of the models -> DIRECTORY <strong>elm_cut_models/</strong></li><li>the reference structures used for the evaluation of the models -> DIRECTORY <strong>ref_capri_curated/</strong></li></ul><p><i>The models in this archive were generated using AlphaFold2-Multimer v2.3</i></p>
Movement of plastic balls in a long-vibrating cylinder: from disorder to structure formation with examples of its instability
<p>Many plastic balls, made from PolyOxyMethylene (POM) and of three different diameters 2, 3 and 4 mm, were used to observe the formation and stability of the structure in ball beds when, after pouring into a plexiglass cylinder, they were subjected to long-term vertical vibrations with frequency 100 Hz. The vibration table Vibrax (Renfert GmbH, Germany), used in the experiment and shown in Fig. 1, can function in two modes: sinusoidal (s) and nonsinusoidal (ns). The vibration table can act at four power levels of the vibrations, selected by an operator using the right knob of the table (see Fig. 1). In the presented series of 43 vibration experiments, always the highest power level was used. </p> <p>Locations of surface balls on all sides of a vibrated cylindrical bed were simultaneously recorded on one video frame thanks to the use of two perpendicular mirrors (see Fig. 1), which enables observation of four images: one of the real cylinder and three of its mirror reflections. An explanation of the scene, as seen by the recording camera, is given in the scheme in Fig. 2. Video names were given in a standard form to inform the user about the most important parameters (more in README.txt).</p> <p> </p>
Dataset for "Structural diversity with varying disorder enables the multicolored display in the longhorn beetle Sulawesiella rafaelae"
<p><strong>Dataset for</strong> "Structural diversity with varying disorder enables the multicolored display in the longhorn beetle <em>Sulawesiella rafaelae</em>"</p> <p>The data is arranged into a .zip folder, containing the following files (.txt, .tif, jpg files). This data and the descriptions below should be read in conjunction with the manuscript and “Supporting Info”, both of which may be found on the <em>iScience</em> homepage.</p> <p>Doi: https://doi.org/10.1016/j.isci.2020.101339</p>
III PhasAGE International Conference - PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins - Lecture
<p>The III PhasAGE International Conference "Multiscale understanding of protein aggregation and biomolecular condensates in aging and disease" brought together members of the PhasAGE consortium as well as outstanding international speakers from multidisciplinary fields dedicated to unraveling the intricacies of protein aggregation and biomolecular condensates in the context of aging and disease. For details on the conference program please see https://phasage.eu/iii-phasage-international-conference/. </p>
Small molecules targeting the structural dynamics of AR-V7 partially disordered protein using deep learning and physics based models.
<p>Partially disordered proteins can contain both stable and unstable secondary structure segments and are involved in various (mis)functions in the cell. The extensive conformational dynamics of partially disordered proteins scaling with extent of disorder and length of the protein hampers the efficiency of traditional experimental and in-silico structure-based drug discovery approaches. Therefore new efficient paradigms in drug discovery taking into account conformational ensembles of proteins need to emerge. In this study, using as a test case the AR-V7 transcription factor splicing variant related to prostate cancer, we present an automated methodology that can accelerate the screening of small molecule binders targeting partially disordered proteins. By swiftly identifying the conformational ensemble of AR-V7, and reducing the dimension of binding-sites by a factor of 90 by applying appropriate physicochemical filters, we combine physics based molecular docking and multi-objective classification machine learning models that speed up the screening of thousands of compounds targeting AR-V7 multiple binding sites. Our method not only identifies previously known binding sites of AR-V7, but also discovers new ones, as well as increases the multi-binding site hit-rate of small molecules by a factor of 17 compared to naive physics-based molecular docking. </p>
Crystal structures of disordered Z-type helices
<p>The X-ray crystal structure of a tetradecamer sequence d(CGCGCGTACGCGCG)2 is presented. The sequence is an alternate<br> pyrimidine-purine repeat and they form disordered, pseudo-continuous left handed Z-type helices. They demonstrate interesting variants of the ‘bundles of columns of helices’ mode of packing.</p>
Crystal structures of disordered Z-type helices
<p>The X-ray crystal structure of a decamer sequence d(CGCGTACGCG) 2 is presented. The sequence is an alternate<br> pyrimidine-purine repeat and they form disordered, pseudo-continuous left handed Z-type helices. They demonstrate interesting variants of the ‘bundles of columns of helices’ mode of packing.</p>
Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders
Open the record for dataset details and reuse information.
Data from: Convergent evolution of disordered lipidic structural color in the fruits of Lantana strigocamara (syn. L. camara hybrid cultivar)
<p><em>Research conducted:</em> The majority of plant colors are produced by anthocyanin and carotenoid pigments, but coloration obtained by nanostructured materials (i.e., structural colors) is increasingly reported in plants. Here, we identify a multilayer photonic structure in the fruits of <em>Lantana strigocamara</em> and compare it to a previously described origin in <em>Viburnum tinus</em>.</p> <p><em>Methods:</em> We used a combination of transmission electron microscopy, serial EM tomography, scanning force microscopy, and optical simulations to characterize the photonic structure in<em> L. strigocamara</em>. We also examine the development of the structure during maturation.</p> <p><em>Key results:</em> We find that the structural color derives from a disordered, multilayered reflector consisting of lipid droplets of ~105 nm that form a plate-like structure in 3D. This structure begins to form early in development and reflects blue wavelengths of light with increasing intensity over time as the structure develops. The lipids used are likely polymers of lipid monomers.</p> <p><em>Main conclusions:</em> <em>Lantana strigocamara</em> is the second origin of a lipid-based photonic structure, convergently evolved with the structure in <em>Viburnum tinus</em>. Chemical differences between the lipids in<em> L. strigocamara</em> and those of <em>V. tinus</em> suggest a distinct evolutionary trajectory with implications for the signaling function of structural colors in fruits.</p>
Ground-state structural disorder and excited-state symmetry breaking in a quadrupolar molecule
<p>The files contains all the data that are shown in the figures of the article:</p> <p>Soederberg, M.; Dereka, B.; Marrocchi, A.; Carlotti, B.; Vauthey, E. Ground-state Structural Disorder and Excited-state Symmetry Breaking in a Quadrupolar Molecule. J. Phys. Chem. Lett. 10 (2019), 10.1021/acs.jpclett.9b01024</p> <p> </p>
Data from: Convergent evolution of disordered lipidic structural color in the fruits of Lantana strigocamara (syn. L. camara hybrid cultivar)
Open the record for dataset details and reuse information.
Static Disorder in Excitation Energies of the Fenna-Matthews-Olson Protein: Structure-Based Theory Meets Experiment
<p>The files contain atomic coordinates of 5200 different conformations of the FMO protein in protein data bank (PDB) format. Each of the 16 zip file contains one directory with 325 PDB files, where each file contains the coordinates of one conformation of the FMO protein. These data were generated with the FIRST/FRODA method as described in Fokas, A.S., Cole, D. and Chin, A. W. Photosynth. Res. 2014, 122, 275-292. The data were used by the present authors to explain the inhomogeneous optical properties of the FMO protein.</p>
Research data for "Origins of structural and electronic transitions in disordered silicon"
<p>This is a dataset related to the publication "Origins of structural and electronic transitions in disordered silicon" (<em>Nature</em> <strong>2021</strong>, <em>589</em>, 59–64). The paper is available online here: https://doi.org/10.1038/s41586-020-03072-z.</p> <p>Three separate .tar.gz archive files are provided:</p> <ul> <li>"coordinates": structural data in (extended) XYZ format including atomic information</li> <li>"ML_DOS_data": original data for the electronic DOS analysis (Fig. 3)</li> <li>"other_potentials": tests with further ML potential models (as described in the Methods section)</li> </ul>
The Production of Jordanian Arabic Passive Structures by Children with Autism Spectrum Disorder
Open the record for dataset details and reuse information.
Supporting Data for the Manuscript "Anionic Disorder and its Impact on the Surface Electronic Structure of Oxynitride Photoactive Semiconductors"
<p>This data repository provides additional data for the manuscript "Anionic disorder and its impact on the surface electronic structure of oxynitride photoactive<br>semiconductors". The data sets comprise the PES raw data files in *.h5 format, the results from RBS/ERDA measurements, and quantification of the surface N:O ratios using TEM in EDX mode.</p> <ul> <li>"BT8c" labels the BTON sample before PEC.</li> <li>"BT8a" labels the BTON sample after PEC.</li> </ul>
Data for "A method for intuitively extracting macromolecular dynamics from structural disorder"
<p>Analyses associated with the manuscript "A method for intuitively extracting macromolecular dynamics from structural disorder".</p>
Salt Induced Transitions in Structural Ensemble of Intrinsically Disordered Proteins
<p>Simulation data and the corrosponding analysis script for the work "<strong>Salt Induced Transitions in Conformational Ensemble of Intrinsically Disordered Proteins</strong> " by <em>Hiranmay Maity, Lipika Baidya </em>and<em> Govardhan reddy</em> are deposited here. </p> <p>Analysis Scripts:</p> <p>The scripts for analysing the simulation data are in analysis_script.zip. The folder contains:</p> <ul> <li> <p>autocorrelation.c : code for calculating end_to_end distance autocorrelation function with time in C.</p> </li> <li> <p>average_property.cpp: code for calculating average property such as radius of gyration (R<sub>g</sub>) from trajectory files in C++.</p> </li> <li> <p>calculate_saxs_kratky.c: code for calculating scattering profile (SAXS and Kratky) from simulation data in C.</p> </li> <li> <p>compute_contact_map.cpp: code for calculating contact map in C.</p> </li> <li> <p>probablity_distribution.c: code for calculating probablity distribution of Rg in C.</p> </li> <li> <p>structure_factor.c: code for calculating structure factor in C.</p> </li> </ul>
Simulation data for "Structural biases in disordered proteins are prevalent in the cell " by Moses & Guadalupe et al. (2023)
<p>This dataset contains complete atomistic ensembles, as reported by Moses & Guadalupe et al. </p> <p><strong>Structural biases in disordered proteins are prevalent in the cell </strong><br> David Moses*, Karina Guadalupe*, Feng Yu, Eduardo Flores, Anthony Perez, Ralph McAnelly, Nora M. Shamoon, Gagandeep Kaur, Estefania Cuevas-Zepeda, Andrea D. Merg, Erik W. Martin, Alex S. Holehouse, Shahar Sukenik</p> <p>For all general inquiries regarding this work, please contact Shahar Sukenik directly. For any specific questions regarding this set of simulations, please contact Alex and Shahar. <br> </p>
Effectiveness of a Structured Physical Rehabilitation Program for Chinese Patients With Depressive Disorders
ClinicalTrials.gov study NCT01536756. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Longitudinal Studies of Brain Structure and Function in MPS Disorders
ClinicalTrials.gov study NCT01870375. IPD Sharing: YES. Countries: 2. Publications: 26.
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Allen Brain Atlas
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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.