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54 results for “protein design”
Data for Stabilization of non-native folds and programmable protein gelation in compositionally designed deep eutectic solvents
<div> <p>Full set of data related to the publication "Stabilization of non-native folds and programmable protein gelation in compositionally designed deep eutectic solvents", published in ACS Nano with DOI:<a title="https://doi.org/10.1021/acsnano.4c01950" href="https://doi.org/10.1021/acsnano.4c01950">10.1021/acsnano.4c01950</a></p> <p> Full details on data treatment and logging are included in the file "DataLogging.pdf". All data use ASCII encoding in delimited .txt files.</p> <p> </p> </div>
Supporting data for the manuscript "Protein quality assessment with graph convolution guided by a loss function designed for high quality decoys"
<p>This dataset provides the predictions of the protein quality<br> assessment method Q_epsilon with respect to CASP13 and CASP14, as well<br> as a snapshot of the github repository providing the code for the<br> method.<br> The format of the file is as follows: The first column represents the<br> target and decoy names in the format <target name>_<decoy name>. The<br> second column is the true GDTTS, and the third column represents the<br> predicted GDTTS by Q_epsilon.</p>
Combining Solid-State NMR with Structural and Biophysical Techniques to Design Challenging Protein-Drug Conjugates
<p>Solid-state NMR spectra (DARR and NCA) of rehydrated freeze-dried free TTR and TTR in the presence of Tafamidis and Taf-PTX</p> <p>Reference citation: Combining Solid-State NMR with Structural and Biophysical Techniques to Design Challenging Protein-Drug Conjugates. Angew Chem Int Ed Engl. 2023 Jun 5:e202303202. doi: 10.1002/anie.202303202. PMID: 37276329.</p>
Dataset for AlphaDesign: A de novo protein design framework based on AlphaFold
<p>This dataset consists of output data from the work reported in: </p> <p>Jendrusch, M., Korbel, J. O., & Sadiq, S. K. (2021). AlphaDesign: A de novo protein design framework based on AlphaFold. bioRxiv.</p> <p> </p> <p> </p>
FASST Structure Database files for "Tertiary motifs as building blocks for the design of protein-binding peptides"
<p>FASST Database files for use in the <a href="https://github.com/swanss/peptide_design">peptide design</a> pipeline.</p> <p>A complete list of structures provided in the databases is provided in the supplementary information of the Protein Science article.</p> <p>Singlechain structures: <a href="https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fpro.4322&file=pro4322-sup-0004-TableS6.txt">pro4322-sup-0004-TableS6.txt</a> (format: PDBID_CHAINID)</p> <p>Multichain structures: <a href="https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fpro.4322&file=pro4322-sup-0005-TableS7.txt">pro4322-sup-0005-TableS7.txt</a> (format: PDBID)</p>
PepBench: Dataset for Protein-Binding Peptide Design
<p>Datasets and splits of protein-peptide complexes benchmark from <a href="https://arxiv.org/abs/2402.13555">PepGLAD</a>.</p> <p>V2 Updates:</p> <ol> <li>The size of ProtFrag augmentation dataset is 70498 instead of 70645. The latest index file has deleted duplicated entries.</li> <li>Clustering results for complexes in training/validation sets are uploaded in train_valid.</li> </ol>
Data for "Designing protein nano-construct in ionic liquid: a boost in efficacy of cytochrome C under stresses"
<p>The dataset provides the raw data for the figures reported in the manuscript entitled "Designing protein nano-construct in ionic liquid: a boost in efficacy of cytochrome C under stresses". Data are provided for silk nanofibrils and protein nano-construct characterization, activity assay of cytochrome c under various conditions, and stability study using CD spectroscopy in .xlsx and .opju format. </p>
Supplementary Data associated with the article "LukProt: A database of eukaryotic predicted proteins designed for investigations of animal origins"
<p>Supplementary Data associated with the article "LukProt: A database of eukaryotic predicted proteins designed for investigations of animal origins" - BUSCO example.</p> <p> </p> <p>National Science Centre of Poland is acknowledged for funding of the project 2020/36/C/NZ8/00081, "The role of glycosylation in the emergence of animal multicellularity", which enabled the creation of this dataset.</p> <p> </p> <p> </p>
Stepwise design of pseudosymmetric protein hetero-oligomers; experimental data
<p>Experimental data presented in the manuscript "Stepwise design of pseudosymmetric protein hetero-oligomers"</p>
Artificial intelligence method to design and fold alpha-helical structural proteins from the primary amino acid sequence
<p>Dataset for paper: Z. Qin, L. Wu, H. Sun, S. Huo, T. Ma, E. Lim, P.-Y. Chen, B. Marelli, M.J. Buehler, Artificial intelligence method to design and fold alpha-helical structural proteins from the primary amino acid sequence, Extreme Mechanics Letters, Vol. 36, 100652, 2020. <a href="https://doi.org/10.1016/j.eml.2020.100652">https://doi.org/10.1016/j.eml.2020.100652</a>.</p> <p>Code: https://github.com/lamm-mit/MNNN/ </p>
Data for: Design of stimulus-responsive two-state hinge proteins
<p>Supplementary information for <strong>Design of stimulus-responsive two-state hinge proteins: </strong>Design scripts, design models, and aw DEER data. </p> <p> </p>
Dataset for Peptide binder design with inverse folding and protein structure prediction
<p>Dataset for a paper on peptide design</p> <p> </p> <p><br> mutated_peptides - results for randomly intriduced mutations in protein-peptide complexes that can be predicted at 2 Å (Figure 1)<br> pdb_peptide - variation in the number of recycles (1-10) for 96 peptides (Figure 1)<br> minibinder - results for the minibinder set (Figure 2)<br> Pfam - results for the Pfam set (Figures 4+5)<br> protein_mpnn - results on protein_mpnn test set (Figure 6)</p> <p> </p> <p> </p>
Data from: Bioinspired design rules for flipping across the lipid bilayer from systematic simulations of membrane protein segments
Open the record for dataset details and reuse information.
Deep learning guided design of dynamic proteins
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Population-based heteropolymer design to mimic protein mixtures
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Molecular Dynamics Simulation Dataset for "Hydrophobic Mismatch Drives Self-Organization of Designer Proteins into Synthetic Membranes"
<p>This repository contains molecular dynamics (MD) simulation data from the study on the self-organization of designer proteins in synthetic membranes. The data includes simulations for different single lipid compositions (DOPC, DPPC, DYPC) denoted as [lipid]-PL* where PL stands for the different TMD constructs. Multi component simulation are named accordingly. The repository provides initial (eqi.gro) and final (prod.gro) coordinates for each simulation. The 'cmd' file in each directory outlines the assembly process of each simulation, and the 'mdp' folder contains all input files for the simulations. </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>
Validation of de novo designed water-soluble and transmembrane proteins by in silico folding and melting
<p>Here are all of the datasets generated and analysed during this study. </p> <p>Here is a breakdown of their content:</p> <ul> <li><strong>8_stranded_transmembrane_barrels.zip</strong> - raw data from Alphafold (3 and 48 recycles), ESMFold and raptor predictions of the 8 stranded TMBs. A file with all the sequences is also given</li> <li><strong>12_stranded_transmembrane_barrels.zip - </strong>raw data from the Alphafold and ESMfold predictions of the 12 stranded TMBs. A file with all the sequences is also given</li> <li><strong>water_soluble_barrels.zip</strong> - raw data from the Alphafold and ESMfold predictions of the water soluble beta barrels (designable and non-designable). A file with all the sequences is also given</li> <li><strong>all design models.zip</strong> - original design models for water-soluble (designable and non-designable), 8-stranded and 12-stranded TMBs</li> </ul> <p> </p> <ul> <li><strong>ESMfold_masking_exp.tar - </strong>this tar file contains all the ESMfold masking experiments performed to the water-soluble, 8 and 12-stranded transmembrane barrels. Inside there are zipped datasets for each masking experiment<br> </li> <li> <p><strong>ziped_raw_csv_files.zip - </strong>raw csv files with all the data necessary to analyse the figures </p> </li> <li> <p><strong>analysis_notebooks.zip </strong>- Jupyter notebooks used to analyse the output prediction data for all figures</p> </li> </ul> <p> </p> <p> </p>
Data for de novo design of buttressed loops for sculpting protein functions
<p>The design scripts for parametric repeat protein generation and buttressed loop are in buttressed_loops.tar.gz</p> <p>All the design models, protein sequences and DNA sequences are in data.tar.gz</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.