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Dataset results
54 results for “protein design”
Raw Data - Design and characterization of mutated variants of the oncotoxic parvoviral protein NS1
<p>Raw data of the Manuscript ''Design and characterization of mutated variants of the oncotoxic parvoviral protein NS1''</p> <p> </p>
Binding networks identify targetable protein pockets for mechanism-based drug design
<p>This repository contains supporting files for the manuscript entitled: Binding networks identify targetable protein pockets for mechanism-based drug design.</p>
Dataset for article: "Massively parallel de novo protein design for targeted therapeutics", DOI: 10.1038/nature23912
<p><strong>"Massively parallel de novo protein design for targeted therapeutics" </strong></p> <p>DOI: 10.1038/nature23912 </p> <p><strong>Supplementary Information</strong>. Archive of designs, Rosetta metrics and experimental results.</p> <p>Authors: <strong>Aaron Chevalier*</strong>, <strong>Daniel-Adriano Silva*</strong>, <strong>Gabriel J. Rocklin*</strong>, Derrick R. Hicks, Renan Vergara, Patience Murapa, Steffen M. Bernard, Lu Zhang, Kwok-ho Lam, Guorui Yao, Christopher D. Bahl, Shin-ichiro Miyashita, Inna Goreshnik, James T. Fuller, Merika T. Koday, Cody Jenkins, Tom Colvin, Lauren Carter, Alan Bohn, Cassie M. Bryan, D. Alejandro Fernández-Velasco, Lance Stewart, Min Dong, Xuhui huang, Rongsheng Jin, Ian A. Wilson, Deborah H. Fuller & <strong>David Baker</strong></p> <p><strong>*These authors contributed equally to this work</strong>.</p> <p>Correspondence to: dabaker@uw.edu</p> <p>Dataset Compiled by D-A.S.</p> <p>Date: 13/Sep/2017</p>
Reproducibility Package for "Design of an allosterically modulated doxycycline and doxorubicin-binding protein"
<p>Files used for MUMBO calculations depicted in the Supplementary Figure 1 of the manuscript "Design of an allosterically modulated doxycycline and doxorubicin-binding protein"</p>
ProteinInvBench: Benchmarking Protein Design on Diverse Tasks, Models, and Metrics
Open the record for dataset details and reuse information.
Structural adaptation of the single-stranded DNA-binding protein C-terminal to DNA metabolizing partners guides in-hibitor design
<p> </p> <ul> <li>Fluorescence anisotropy metadata and polarization values </li> <li>Isotermal titration calorimetry raw files (protein-ligand and background titrations)</li> <li>Input files for PRALINE calculation in FASTA format</li> <li>CSV file containing the SSB sequences in SMILES format and binding data</li> <li>The input files for the ExoI-bound wtSSB-Ct, E1-sSSB-Ct, and E2-sSSB-Ct and RecO-bound wtSSB-Ct, R1-sSSB-Ct, and R2-sSSB-Ct together with the corresponding trajectory files </li> </ul>
Data associated with the publication "Assembling membraneless organelles from de novo designed proteins"
<p>Raw data used in the manuscript "Assembling membraneless organelles from de novo designed proteins"</p>
Modelling the Interaction Between Rationally-designed Synthetic Model Viral Protein Immunogens
ClinicalTrials.gov study NCT03816137. IPD Sharing: YES. Countries: 1. Publications: 1.
An Exploratory Pilot Study in Healthy Volunteers to Assess the Parameters for the Design of Bioequivalence Studies on Moderately Lipophilic, Moderately to Highly Protein Bound Drugs Using Dermal Open
ClinicalTrials.gov study NCT03613207. IPD Sharing: UNDECIDED. Countries: 1. Publications: 5.
Data from: Computational design of protein-based inhibitors of Plasmodium vivax subtilisin-like 1 protease
Open the record for dataset details and reuse information.
Data for: Reconfigurable asymmetric protein assemblies through implicit negative design
<p>Supplementary Information for <strong>Reconfigurable asymmetric protein assemblies through implicit negative design: </strong>design scripts, design models and sequence information </p> <p> </p> <p>Authors:<strong> Danny D. Sahtoe*, Florian Praetorius*, </strong>Alexis Courbet, Yang Hsia, Basile I.M. Wicky, Natasha I. Edman, Lauren M. Miller, Bart J. R. Timmermans, Justin Decarreau, Hana M. Morris, Alex Kang, Asim K. Bera, David Baker</p> <p><strong>* These authors contributed equally</strong></p> <p>Correspondence to: dabaker@uw.edu</p>
A generic framework for hierarchical de novo protein design
<p><strong>A small MASTER database</strong> that (most of the time) will be enough for most of the design tasks. The data includes the PDB files <em>master_pdb</em>, PDS files <em>maps</em>, structure fragments <em>frags</em>, ABEG0 torsions <em>master_abego.fa.gz</em>, and secondary structure <em>master_sse.fa.gz</em>.</p>
Inverse design of viral infectivity-enhancing peptide fibrils from continuous protein-vector embeddings
<p>The Tables S3 - S5 are a supplement for the article "Inverse design of viral infectivity-enhancing peptide fibrils from continuous protein-vector embeddings" uploaded as a Preprint in ChemRxiv DOI: 10.26434/chemrxiv-2023-1kqm3</p>
Stepwise design of pseudosymmetric protein hetero-oligomers; design models
<p>Design models for the associated publication</p>
Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 1]
GEO Series GSE133365. synthetic construct. 32 samples. Type: Other.
Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 2]
GEO Series GSE133366. synthetic construct. 12 samples. Type: Other.
Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 3]
GEO Series GSE133367. Homo sapiens; Bos taurus; synthetic construct. 114 samples. Type: Other.
RNA features governing zinc finger antiviral protein sensitivity enable attenuated virus design
GEO Series GSE208611. synthetic HIV-1; Homo sapiens. 4 samples. Type: Other.
Computational design of sequence-specific DNA-binding proteins
GEO Series GSE237017. Homo sapiens; synthetic construct. 12 samples. Type: Other.
Peptide design by optimization on a data-parameterized protein interaction landscape
GEO Series GSE118147. Saccharomyces cerevisiae. 3 samples. Type: Other.
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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.