Protein data

Published Data

General useful data sources

The Human Protein Atlas (HPA) provides open access to protein expression data across human organs, tissues and cells. This protein resource is organized into focused sections for tissue expression, subcellular expression, proteins in the brain or in blood, proteins related to pathology and metabolic pathways. A special page of HPA has been dedicated to human proteins and SARS-CoV-2.
PRIDE PRoteomics IDEntifications (PRIDE) Archive database - centralized, standards compliant, public data repository for mass spectrometry proteomics data, including protein and peptide identifications and the corresponding expression values, post-translational modifications and supporting mass spectra evidence (both as raw data and peak list files). PRIDE is a core member in the ProteomeXchange (PX) consortium, which provides a standardised way for submitting mass spectrometry based proteomics data to public-domain repositories. Datasets are submitted to ProteomeXchange via PRIDE and are handled by expert bio-curators. All PRIDE public datasets can also be searched in ProteomeCentral, the portal for all ProteomeXchange datasets.
PROTEOMEEXCHANGE Consortium - globally coordinated standard data submission and dissemination pipelines involving the main proteomics repositories.
MassIVE - a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange accessions to satisfy publication requirements.

Data available on the European COVID-19 Data Portal

Sequence, functional and classification data on SARS-CoV-2 and host proteins

Data available from research groups in Sweden

The list of available data on this Portal was curated manually until February 2022. After February 2022, we instead began to use a script to query the Europe PMC database (making use of their API) in order to locate relevant publications. We only include data from publications about COVID-19/SARS-CoV-2 that BOTH involve at least one author affiliated with a Swedish research institution AND openly share reusable data and/or code. The code used for the query is written in Python and, as with all of our code, it is openly available in GitHub. We welcome others to reuse it and to repurpose it for other pathogens.

The lists of available data may not be exhaustive as the script used to generate it does not search for every possible database/repository. If you find that a dataset is missing, or that the information related to it is incorrect, please get in touch with us

Last updated: 2024-09-04

Data types

All data types (290)

Biochemistry data (34)

Drug discovery data (15)

Genomics & transcriptomics data (84)

Health data (102)

Imaging data (7)

Other data (47)

Protein data (48)

Public health data (68)

Serology data (22)

Social science and humanities data (64)

Publication	Available dataset and code
Emergence of SARS-CoV-2 omicron variant JN.1 in Tamil Nadu, India - Clinical characteristics and novel mutations Selvavinayagam S. T., Sankar S., Yong Y. K., Murugesan A., et al (2024) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s41598-024-68678-z	Structure of the Axl kinase domain in complex with a macrocyclic inhibitor data Protein Data Bank: 5u6b Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 data Protein Data Bank: 6m0j Plasmodium falciparum reticulocyte-binding protein homologue 5 (PfRH5) bound to basigin data Protein Data Bank: 4u0q Crystal Structure of a fragment of DC-SIGNR (containing the carbohydrate recognition domain and two repeats of the neck). data Protein Data Bank: 1xar
Mammalian cell display with automated oligo design and library assembly allows for rapid residue level conformational epitope mapping Thalén N. B., Karlander M., Lundqvist M., Persson H., et al (2024) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s42003-024-06508-8	Epitope mapping of analytes binding RBD code Github Flow cytometry data for: Mammalian cell display with automated oligo design and library assembly allows for rapid residue level conformational epitope mapping data figshare Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab data Protein Data Bank: 6yla Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2 data Protein Data Bank: 6vw1 Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor data Protein Data Bank: 2ajf Nucleotide Sequences data European Nucleotide Archive: MK988448.1
Spike deep mutational scanning helps predict success of SARS-CoV-2 clades Dadonaite B., Brown J., McMahon T. E., Farrell A. G., et al (2024) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s41586-024-07636-1	LY-CoV1404 neutralising antibody against SARS-CoV-2 data Protein Data Bank: 7mmo Structure of the SARS-CoV-2 XBB.1 spike glycoprotein (closed-2 state) data Protein Data Bank: 8iot Complex of SARS-CoV-2 receptor binding domain with the Fab fragments of two neutralising antibodies data Protein Data Bank: 6xdg Structure of SARS-CoV-2 XBB.1 spike glycoprotein in complex with ACE2 (1-up state) data Protein Data Bank: 8iou Deep mutational scanning of SARS-CoV-2 XBB.1.5 spike using a barcoded lentiviral platform data Supplementary Data Mass photometry analysis of Spike:ACE2 binding code Github SARS-CoV-2_XBB.1.5_RBD_DMS code Github Pipeline for analysing deep mutational scanning (DMS) of viral entry proteins (VEPs) code Github SARS-CoV-2_Omicron_BA.2_spike_ACE2_binding code Github SARS-CoV-2_XBB.1.5_spike_DMS code Github SARS-CoV-2_XBB.1.5_spike_DMS: SARS-CoV-2_XBB.1.5_spike_DMS-paper data Zenodo
Proteome profiling of home-sampled dried blood spots reveals proteins of SARS-CoV-2 infections Fredolini C., Dodig-Crnković T., Bendes A., Dahl L., et al (2024) Springer Science and Business Media LLC DOI: 10.1038/s43856-024-00480-4	Protein levels obtained from dried blood spot (DBS) samples. data Figshare Data from multiplexed serology assays to determine IgG and IgM levels against several versions of SARS-CoV-2 proteins. Samples obtained from dried blood spots (DBS). data Figshare Code for the analysis and visualisation of proteome data from home-sampled dried blood spots. code GitHub
Synthetic coevolution reveals adaptive mutational trajectories of neutralizing antibodies and SARS-CoV-2 Ehling R. A., Minot M., Overath M. D., Sheward D. J., et al (2024) Cold Spring Harbor Laboratory DOI: 10.1101/2024.03.28.587189	A protein language machine learning model that predicts antibody escape to receptor binding domain variants. code GitHub
Design, structure and plasma binding of ancestral β-CoV scaffold antigens Hueting D., Schriever K., Sun R., Vlachiotis S., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41467-023-42200-x	Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein (map). data Electron Microscopy Data Bank: EMD-15475 Structure of the Ancestral Scaffold Antigen-6 of Coronavirus Spike protein (map). data Electron Microscopy Data Bank: EMD-15482 Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein (atomic coordinates). data Protein Data Bank: 8AJA Structure of the Ancestral Scaffold Antigen-6 of Coronavirus Spike protein (atomic coordinates). data Protein Data Bank: 8AJL
De novo design of anti-variant COVID-19 vaccine Goswami A., Kumar M., Ullah S., Gore M. M. (2023) Oxford University Press (OUP) DOI: 10.1093/biomethods/bpad021	The designed vaccine structure for Vacdeltm. data Protein Model Database: PM0084589 The designed vaccine structure for VacFL. data Protein Model Database: PM0084590
Comprehensive proteomics and meta-analysis of COVID-19 host response Babačić H., Christ W., Araújo J. E., Mermelekas G., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41467-023-41159-z	Results of the meta-analysis are available in a Shiny app. data In-depth serum proteomics of hospitalized COVID-19 patients and PCR-negative healthy controls with HiRIEF LC-MS/MS data ProteomeXchange: PXD037486 Mass-spectrometry proteomics of Calu-3 cell lines infected with SARS-CoV-2, in comparison to non-infected and UV mock-treated cell lines data ProteomeXchange: PXD037451 Mass-spectrometry phosphoproteomics of Calu-3 cell lines infected with SARS-CoV-2, in comparison to non-infected and UV mock-treated cell lines data ProteomeXchange: PXD040982 Custom code for the Nextflow proteomics workflow code GitHub R code used for analyses code GitHub
Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets Mihalič F., Benz C., Kassa E., Lindqvist R., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41467-023-41312-8	Library designs including the proteins, peptides and statistics data
Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis Hartman E., Scott A. M., Karlsson C., Mohanty T., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41467-023-41146-4	AKI DIA samples for generalized peakgroup scoring model application data PRIDE: PXD038394 A time-resolved proteomic and prognostic map of COVID-19 data PRIDE: PXD025752 Olink Dataset data Figshare 56 samples from acute kidney injury patients (DIA-MS septic AKI dataset). data PRIDE: PXD044264 Biologically Informed Neural Network (BINN) code code GitHub InfectionMedicineProteomics/BINN: First release code Zenodo DE-score algorithm has been implemented into the data processing package DPKS code GitHub
Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses Pushparaj P., Nicoletto A., Castro Dopico X., Sheward D. J., et al (2023) Frontiers Media SA DOI: 10.3389/fviro.2023.1128253	The HC sequences of CAB-F52 anti-SARS-CoV-2 immunoglobulin heavy chain variable region mRNA data GenBank: ON086926 The LC sequences of CAB-F52 anti-SARS-CoV-2 immunoglobulin heavy chain variable region mRNA data GenBank: ON086941 The hydrogen–deuterium exchange mass spectrometry data data ProteomeXchange: PXD031945
Proteome-wide Mendelian randomization implicates nephronectin as an actionable mediator of the effect of obesity on COVID-19 severity Yoshiji S., Butler-Laporte G., Lu T., Willett J. D. S., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s42255-023-00742-w	Summary statistics related to body mass index (BMI) data Summary statistics on plasma proteome from the deCODE study data Summary statistics related to COVID-19 outcomes data Long Read RNASeq data data GTEx: phs000424.v9 Body fat percentage data data OpenGWAS: ukb-b-8909 Whole body fat mass data data OpenGWAS: ukb-b-19393 Whole body fat-free mass data data OpenGWAS: ukb-b-13354 scRNA-seq data of COVID-19 lung autopsy samples data Custom analysis codes code GitHub
Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development Islam M. A., Shahi S., Marzan A. A., Amin M. R., et al (2023) Frontiers Media SA DOI: 10.3389/fphar.2023.1090717	Supplementary material including information on proteomics, mutations, T-cell epitope prediction, and much more, including accession numbers for other open data sources data
Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies Pushparaj P., Nicoletto A., Sheward D. J., Das H., et al (2023) Elsevier BV DOI: 10.1016/j.immuni.2022.12.005	Individualised IGHV Genotype Sequences of 14 SARS-CoV-2 Convalescent Donors data Figshare Mass spectrometry raw files and HDX analysis data ProteomeXchange SARS Cov2 Spike in 1-up conformation complex with Fab47 data PDB: 8A99 SARS CoV2 Spike in the 2-up state in complex with Fab47 data PDB: 8A94 SARS Cov2 Spike RBD in complex with Fab47 data PDB: 8A96 SARS Cov2 Spike in 1-up conformation complex with Fab47 data Electron Microscopy Data Bank: EMD-15273 SARS CoV2 Spike in the 2-up state in complex with Fab47 data Electron Microscopy Data Bank: EMD-15269 SARS Cov2 Spike RBD in complex with Fab47 data Electron Microscopy Data Bank: EMD-15271 Supplemental data, including Cryo-EM models data Mendeley
Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level Zhu R., Canena D., Sikora M., Klausberger M., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41467-022-35641-3	Models of SARS-CoV-2 virus spike protein bound to 1-3 of ACE2 receptors embedded in lipid nanodisks. data Zenodo Code for simulation of high speed AFM imaging. code GitHub
The screening and evaluation of potential clinically significant HIV drug combinations against the SARS-CoV-2 virus Tomić D., Davidović D., Szasz A. M., Rezeli M., et al (2022) Elsevier BV DOI: 10.1016/j.imu.2021.100529	Results of the efficacy of FDA approved antiviral drugs on SARS-CoV-2 spike glycoprotein. data The Vini in silico model of cancer. code GitHub
The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19 Consiglio C. R., Cotugno N., Sardh F., Pou C., et al (2022) Elsevier BV DOI: 10.1016/j.cell.2020.09.016	Data organised by figures presented in the article. data Mendeley Plasma protein expression (Olink - NPX values), FACS, Autoantibodies. data Figshare Scripts to complete analyses and produce figures. code GitHub
A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process Noske G., Nakamura A., Gawriljuk V., Fernandes R., et al (2022) Elsevier BV DOI: 10.1016/j.jmb.2021.167118	7KFI SARS-CoV-2 Main protease immature form - apo structure data Protein Data Bank: 7KFI 7MBG SARS-CoV-2 Main protease in orthorhombic space group data Protein Data Bank: 7MBG 7KPH SARS-CoV-2 Main Protease in mature form data Protein Data Bank: 7KPH 7N6N SARS-CoV-2 Main protease C145S mutant in complex with N and C-terminal residues data Protein Data Bank: 7N6N 7LFE SARS-CoV-2 Main protease immature form - F2X Entry Library E03 fragment data Protein Data Bank: 7LFE 7LDX SARS-CoV-2 Main protease immature form - F2X Entry Library E06 fragment data Protein Data Bank: 7LDX 7LFP SARS-CoV-2 Main protease immature form - F2X Entry Library G05 fragment data Protein Data Bank: 7LFP 7KVL SARS-CoV-2 Main protease immature form - FMAX Library E01 fragment data Protein Data Bank: 7KVL 7N5Z SARS-CoV-2 Main protease C145S mutant data Protein Data Bank: 7N5Z 7KVR SARS-CoV-2 Main protease immature form - FMAX Library E09 fragment data Protein Data Bank: 7KVR
Structural and biochemical characterization of in vivo assembled Lactococcus lactis CRISPR-Csm complex Sridhara S., Rai J., Whyms C., Goswami H., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s42003-022-03187-1	Structure of the lactococcus lactis csm ctr_4:3 crispr-cas complex data PDB: 6XN3 Structure of the lactococcus lactis csm apo- crispr-cas complex data PDB: 6XN5 Structure of the lactococcus lactis csm ctr_3:2 crispr-cas complex data PDB: 6XN4 structure of the lactococcus lactis csm ntr crispr-cas complex data PDB: 6XN7
Improved prediction of protein-protein interactions using AlphaFold2 Bryant P., Pozzati G., Elofsson A. (2022) Springer Science and Business Media LLC DOI: 10.1038/s41467-022-28865-w	Raw data and predicted PDB files data FigShare: 16866202.v1
Molecular mechanism of inhibiting the SARS-CoV-2 cell entry facilitator TMPRSS2 with camostat and nafamostat Hempel T., Raich L., Olsson S., Azouz N. P., et al (2022) Royal Society of Chemistry (RSC) DOI: 10.1039/d0sc05064d	Structural ensembles of camostat, GBPA, and nafamostat code GitHub
Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort Carapito R., Li R., Helms J., Carapito C., et al (2022) American Association for the Advancement of Science (AAAS) DOI: 10.1126/scitranslmed.abj7521	Proteomics data data ProteomeXchange: PXD025265 RNA-seq datasets data Gene Expression Omnibus: GSE172114 Code to perform classification and structural causal modeling code Zenodo
A proteomic survival predictor for COVID-19 patients in intensive care Demichev V., Tober-Lau P., Nazarenko T., Lemke O., et al (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pdig.0000007	Protein quantities table along with the associated metadata data Input proteomics data for training machine learning models data Scripts training machine learning models code Mass spectrometry proteomics data used for survival analysis data ProteomeXchange Consortium: PXD029009
A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo Hanke L., Das H., Sheward D. J., Perez Vidakovics L., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41467-021-27610-z	cryo-EM density maps data Electron Microscopy Data Bank: EMD-12561 cryo-EM density maps data Electron Microscopy Data Bank: EMD-12465 Atomic coordinates data Protein Data Bank: 7NS6 Atomic coordinates data Protein Data Bank: 7NLL Source Data for Study data
Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16 Kozielski F., Sele C., Talibov V. O., Lou J., et al (2022) Royal Society of Chemistry (RSC) DOI: 10.1039/D1CB00135C	Protein model data Protein Data Bank: 7ORW Protein model data Protein Data Bank: 7ORV Protein model data Protein Data Bank: 7ORU Protein model data Protein Data Bank: 7ORR Crystallographic fragment screen data Zenodo
Differential Effect of SARS-CoV-2 Spike Glycoprotein 1 on Human Bronchial and Alveolar Lung Mucosa Models: Implications for Pathogenicity Rahman M., Irmler M., Keshavan S., Introna M., et al (2021) MDPI AG DOI: 10.3390/v13122537	Expression profiling by high throughput sequencing data Gene Expression Omnibus: GSE185657
1H, 13C and 15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution Agback T., Dominguez F., Frolov I., Frolova E. I., et al (2021) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0251834#sec006	Chemical shifts of full-length SARS-CoV-2 data BioMagResBank: 50915
Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis Hober A., Tran-Minh K. H., Foley D., McDonald T., et al (2021) eLife Sciences Publications, Ltd DOI: 10.7554/eLife.70843	Proteomics data data ProteomeXchange: PXD026366 Mass spectrometry data generated data
Advances and Utility of the Human Plasma Proteome Deutsch E. W., Omenn G. S., Sun Z., Maes M., et al (2021) American Chemical Society (ACS) DOI: 10.1021/acs.jproteome.1c00657	Union of proteins in both the plasma and blood extracellular vesicle PeptideAtlas builds data
Blue Biotechnology: Computational Screening of Sarcophyton Cembranoid Diterpenes for SARS-CoV-2 Main Protease Inhibition Ibrahim M. A. A., Abdelrahman A. H. M., Atia M. A. M., Mohamed T. A., et al (2021) MDPI AG DOI: 10.3390/md19070391	All data are included in the article or supplementary material (Sarcophyton cembranoid diterpenes metabolites). data
An artificial neural network approach integrating plasma proteomics and genetic data identifies PLXNA4 as a new susceptibility locus for pulmonary embolism Razzaq M., Iglesias M. J., Ibrahim-Kosta M., Goumidi L., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41598-021-93390-7	Proteomics dataset based on plasma samples from 1,388 subjects. data Zenodo
Virological and immunological features of SARS-CoV-2-infected children who develop neutralizing antibodies Cotugno N., Ruggiero A., Bonfante F., Petrara M. R., et al (2021) Elsevier BV DOI: 10.1016/j.celrep.2021.108852	Data required to produce the figures, includes data on proteomics and immunology data Mendeley R code for multi-omics factor analyses, correlations, and plots code GitHub
Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium Mehregan A., Pérez-Conesa S., Zhuang Y., Elbahnsi A., et al (2021) Cold Spring Harbor Laboratory DOI: 10.1101/2021.05.28.446179	Biophysical characterisation of the SARS-CoV-2 E protein. data Zenodo
Type-I interferon signatures in SARS-CoV-2 infected Huh7 cells Chen X., Saccon E., Appelberg K. S., Mikaeloff F., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41420-021-00487-z	Raw mass spectromic data. data ProteomeXchange: PXD023450 bioinformatic analysis codes. data GitHub
Ultra-fast proteomics with Scanning SWATH Messner C. B., Demichev V., Bloomfield N., Yu J. S. L., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41587-021-00860-4	The data generated for the benchmarks and the drug response screen in yeast data ProteomeXchange: PXD023613 Open-source algorithms made available through the DIA–NN software suite code GitHub
Proteomic blood profiling in mild, severe and critical COVID-19 patients Patel H., Ashton N. J., Dobson R. J. B., Andersson L., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41598-021-85877-0	Proteomic data data BioStudies: S-BSST416 Application related to proteomic data analysis code Zenodo Code behind application related to proteomic data analysis code GitHub
Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape Koenig P., Das H., Liu H., Kümmerer B. M., et al (2021) American Association for the Advancement of Science (AAAS) DOI: 10.1126/science.abe6230	Data generated/analysed are in the article or supplementary materials. data Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobodies VHH E and U. data Protein Data Bank: 7KN5 Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH V and antibody Fab CC12.3. data Protein Data Bank: 7KN6 Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH W and antibody Fab CC12.3. data Protein Data Bank: 7KN7 SARS-CoV-2 spike in complex with nanobodies E. data Protein Data Bank: 7KSG Nanobody E bound to Spike-RBD in a localized reconstruction. data Protein Data Bank: 7B14 SARS-CoV-spike with two RBDs up bound to VHH V on all RBDs. data Protein Data Bank: 7B11 SARS-CoV-spike bound to two neutralising nanobodies. data Protein Data Bank: 7B18 SARS-CoV-spike RBD bound to two neutralising nanobodies. data Protein Data Bank: 7B17 SARS-CoV-2 spike in complex with nanobodies E. data Electron Microscopy Data Bank: EMD-23018 Nanobody E bound to Spike-RBD in a localized reconstruction. data Electron Microscopy Data Bank: EMD-11978 SARS-CoV-spike bound to two neutralising nanobodies. data Electron Microscopy Data Bank: EMD-11981 SARS-CoV-spike RBD bound to two neutralising nanobodies. data Electron Microscopy Data Bank: EMD-11980 Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape. data BioProject: PRJNA679438
Human species D adenovirus hexon capsid protein mediates cell entry through a direct interaction with CD46 Persson B. D., John L., Rafie K., Strebl M., et al (2020) Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.2020732118	Crystal Structure of Human Adenovirus 56 Fiber Knob. data Protein Data Bank: 7AJP
Novel Broad-Spectrum Antiviral Inhibitors Targeting Host Factors Essential for Replication of Pathogenic RNA Viruses Tampere M., Pettke A., Salata C., Wallner O., et al (2020) MDPI AG DOI: 10.3390/v12121423	Thermal Proteome Profiling dataset from Hazara virus infected SW13 cells treated with DMSO or antiviral inhibitor 20 µM TH6744 data Figshare Antiviral screening; Dose-response treatment of TH6744 and TH3289; List of proteins from 2D-TPP analysis in U87 cells (FDR); List of proteins from 2D-TPP analysis in U87 cells (Fold-change); Uniprot annotation of overlapping TPP-TR and 2D-TPP hits data Raw mass spectrometry data data ProteomeXchange Consortium: PXD021494
Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2 Custódio T. F., Das H., Sheward D. J., Hanke L., et al (2020) Springer Science and Business Media LLC DOI: 10.1038/s41467-020-19204-y	Microscale thermophoresis (MST) and biolayer interferometry (BLI) data. data GitHub Synthetic nanobody Sybody 23 (Sy23). data SASBDB: SASDJF4 SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD). data SASBDB: SASDJG4 SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD) bound to the synthetic nanobody Sybody 23 (Sy23). data SASBDB: SASDJH4 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23). data Electron Microscopy Data Bank: EMD-11616 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation. data Electron Microscopy Data Bank: EMD-11617 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23). data Protein Data Bank: 7A25 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation. data Protein Data Bank: 7A29 Sequences of all the selected sybodies. data Source data. data
Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2 Rogstam A., Nyblom M., Christensen S., Sele C., et al (2020) MDPI AG DOI: 10.3390/ijms21197375	Nonstructural protein 10 (nsp10) from SARS CoV-2, 1.58Å resolution. data Protein Data Bank: 6ZPE Nonstructural protein 10 (nsp10) from SARS CoV-2, 2.55Å resolution. data Protein Data Bank: 6ZCT Nsp10 unfolding temperatures determined by DSF. data
Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19 Sekine T., Perez-Potti A., Rivera-Ballesteros O., Strålin K., et al (2020) Elsevier BV DOI: 10.1016/j.cell.2020.08.017	All data generated during the study (predicted binding affinities, donor characteristics, sample information, and some analyses) are available in the article. data
MAIT cell activation and dynamics associated with COVID-19 disease severity Parrot T., Gorin J., Ponzetta A., Maleki K. T., et al (2020) American Association for the Advancement of Science (AAAS) DOI: 10.1126/sciimmunol.abe1670	Curated flow cytometry data are available for exploration via the Karolinska COVID-19 Immune Atlas. data All other data are available in the article itself or the supplementary materials. data
An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction Hanke L., Vidakovics Perez L., Sheward D. J., Das H., et al (2020) Springer Science and Business Media LLC DOI: 10.1038/s41467-020-18174-5	Sequence of Ty1. data GenBank: MT784731 Bio layer interferometry (BLI) data. data GitHub Isothermal titration calorimetry (ITC) data. data GitHub Next generation sequencing (NGS) data. data BioProject: PRJNA638614 Jupyter notebooks to reproduce next generation sequencing (NGS) data. code GitHub Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1). data Electron Microscopy Data Bank: EMD-11526 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1). data Protein Data Bank: 6ZXN
Systems-Level Immunomonitoring from Acute to Recovery Phase of Severe COVID-19 Rodriguez L., Pekkarinen P. T., Lakshmikanth T., Tan Z., et al (2020) Elsevier BV DOI: 10.1016/j.xcrm.2020.100078	Raw mass cytometry data and the Olink protein data generated during this study. data Immunoglobulin G (IgG) data. data SARS-CoV2 longitudinal systems-level analyses code. data GitHub
Natural killer cell immunotypes related to COVID-19 disease severity Maucourant C., Filipovic I., Ponzetta A., Aleman S., et al (2020) American Association for the Advancement of Science (AAAS) DOI: 10.1126/sciimmunol.abd6832	Curated flow cytometry data available via the Karolinska COVID-19 Immune Atlas. data Raw data, clinical characteristics of patients, and various results files are available in supplementary data. data
Acute necrotizing encephalopathy with SARS-CoV-2 RNA confirmed in cerebrospinal fluid Virhammar J., Kumlien E., Fällmar D., Frithiof R., et al (2020) Ovid Technologies (Wolters Kluwer Health) DOI: 10.1212/wnl.0000000000010250	Proteomics data. data Dryad
Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells Appelberg S., Gupta S., Svensson Akusjärvi S., Ambikan A. T., et al (2020) Informa UK Limited DOI: 10.1080/22221751.2020.1799723	Raw RNAseq data data BioProject Proteomics data data Zenodo All pre-processing and analysis code code GitHub