Biochemistry data

Published Data

On our portal, “Biochemistry” has a broad meaning, including cell- and plasma profiling with, for example, biomarker concentrations in plasma.

General useful data sources

Small molecule related data can be found in ChEMBL. ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.
IntAct Molecular Interaction Database - a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available. The database is manually curated; content is added by curators at the EMBL-EBI and partner organizations.
REACTOME - open-source, open access, manually curated and peer-reviewed pathway database. The goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic and clinical research, genome analysis, modeling, systems biology and education.

Data available on the European COVID-19 Data Portal

COVID-19 pathways, interactions, complexes, targets and compounds

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)

Public health data (68)

Serology data (22)

Social science and humanities data (64)

Publication	Available dataset and code
SARS-CoV-2 antibodies from children exhibit broad neutralization and belong to adult public clonotypes Wall S. C., Suryadevara N., Kim C., Shiakolas A. R., et al (2023) Elsevier BV DOI: 10.1016/j.xcrm.2023.101267	Raw sequence reads related to SARS-CoV-2 antibodies from children exhibiting broad neutralisation. data Sequence Read Archive: PRJNA1014462 SARS-CoV-2 spike in complex with Fab 71281-33. data Electron Microscopy Databank: EMD-41075 SARS-CoV-2 spike in complex with Fab 71281-33 (2). data Electron Microscopy Databank: EMD-41076
Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency Le Voyer T., Parent A. V., Liu X., Cederholm A., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41586-023-06717-x	Raw RNA sequence reads produced when patient whole blood samples were analysed by RNA sequencing in order to monitor global changes in transcript abundance levels post-interferon treatment. data NCBI database: PRJNA989123
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
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
Characterising information loss due to aggregating epidemic model outputs Sherratt K., Srivastava A., Ainslie K., Singh D. E., et al (2023) Cold Spring Harbor Laboratory DOI: 10.1101/2023.07.05.23292245	Data used in modelling, including location and population size. data GitHub Data processing code in R is available on Github code GitHub
Vaccine-induced correlate of protection against fatal COVID-19 in older and frail adults during waves of neutralization-resistant variants of concern: an observational study Vikström L., Fjällström P., Gwon Y., Sheward D. J., et al (2023) Elsevier BV DOI: 10.1016/j.lanepe.2023.100646	Data processing code in R is available on Github data GitHub
Sustained IFN signaling is associated with delayed development of SARS-CoV-2-specific immunity Brunet-Ratnasingham E., Morin S., Randolph H. E., Labrecque M., et al (2023) Cold Spring Harbor Laboratory DOI: 10.1101/2023.06.14.23290814	Clinical data and biobanks samples from 250 critically ill COVID-19 patients. Appropriate permits are required for access. data Figshare Data from the BQC-19 repository is available after appropriate permissions and data access agreements data BQC-19
Single-Virus Fusion Measurements Reveal Multiple Mechanistically Equivalent Pathways for SARS-CoV-2 Entry Sengar A., Cervantes M., Bondalapati S. T., Hess T., et al (2023) American Society for Microbiology DOI: 10.1128/jvi.01992-22	Movies and data to accompany the study data zenodo: 7826331 Image and time series analysis code written in MATLAB is available on GitHub code GitHub
Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 lineage transition in the Swedish population reveals increased viral RNA levels in BA.2 cases Lentini A., Pereira A., Winqvist O., Reinius B. (2022) Elsevier BV DOI: 10.1016/j.medj.2022.07.007	Assembled SARS-CoV-2 genomes data GISAID: EPI_ISL_11414777-11415389 and EPI_ISL_11450500-11450677 Raw sequencing data data ArrayExpress: E-MTAB-11650 Computational code code GitHub
Whole blood DNA methylation analysis reveals respiratory environmental traits involved in COVID-19 severity following SARS-CoV-2 infection Barturen G., Carnero-Montoro E., Martínez-Bueno M., Rojo-Rello S., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41467-022-32357-2	Genotype data generated (SPGRX cohort) data EGA: EGAS00001005304 Methylation data data Gene Expression Omnibus: GSE179325
JAK inhibition reduces SARS-CoV-2 liver infectivity and modulates inflammatory responses to reduce morbidity and mortality Stebbing J., Sánchez Nievas G., Falcone M., Youhanna S., et al (2022) American Association for the Advancement of Science (AAAS) DOI: 10.1126/sciadv.abe4724	RNA-seq of SARS-CoV-2-infected human primary hepatocyte-derived spheroids upon interferon a2 and baricitinib treatment. data ArrayExpress: E-MTAB-9711 Patient information are contained in the paper and supplementary information. data
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
Beta RBD boost broadens antibody-mediated protection against SARS-CoV-2 variants in animal models Sheward D. J., Mandolesi M., Urgard E., Kim C., et al (2021) Elsevier BV DOI: 10.1016/j.xcrm.2021.100450	Data from clinical trial registries used in the study code GitHub
Acquired olfactory loss alters functional connectivity and morphology Iravani B., Peter M. G., Arshamian A., Olsson M. J., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41598-021-95968-7	Data cannot be shared publicly, but applications can be made for access. data
Single-Dilution COVID-19 Antibody Test with Qualitative and Quantitative Readouts Bortz R. H., Florez C., Laudermilch E., Wirchnianski A. S., et al (2021) American Society for Microbiology DOI: 10.1128/mSphere.00224-21	Input data related to ELISA tests. data GitHub Code related to modelling antibody titer quantification from single dilution points. 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
Innate lymphoid cell composition associates with COVID‐19 disease severity García M., Kokkinou E., Carrasco García A., Parrot T., et al (2021) Wiley DOI: 10.1002/cti2.1224	Karolinska KI/K Covid19 Immune atlas. data
Efficacy and tolerability of bevacizumab in patients with severe Covid-19 Pang J., Xu F., Aondio G., Li Y., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41467-021-21085-8	Raw data with demographic and clinical characteristics of the patients, progress of treatment and control groups. data Figshare All relevant codes used in SAS software for statistical analysis. code Figshare
SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 immunogenicity in baboons and protection in mice Tian J., Patel N., Haupt R., Zhou H., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41467-020-20653-8	Source data behind study. data
Sputum ACE2, TMPRSS2 and FURIN gene expression in severe neutrophilic asthma Kermani N. Z., Song W., Badi Y., Versi A., et al (2021) Springer Science and Business Media LLC DOI: 10.1186/s12931-020-01605-8	Data cannot be shared publicly, but applications can be made for access. data
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
Broadly Active Antiviral Compounds Disturb Zika Virus Progeny Release Rescuing Virus-Induced Toxicity in Brain Organoids Pettke A., Tampere M., Pronk R., Wallner O., et al (2020) MDPI AG DOI: 10.3390/v13010037	Data are available in the article and supplementary materials (effect of novel antiviral compounds against ZIKV in several cell models). data
Mechanisms of a Sustained Anti‐inflammatory Drug Response in Alveolar Macrophages Unraveled with Mathematical Modeling Nyman E., Lindh M., Lövfors W., Simonsson C., et al (2020) Wiley DOI: 10.1002/psp4.12568	Experimental data are in the supplementary material data Code for macrophage model (matlab) code GitLab
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
Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy Wacker A., Weigand J. E., Akabayov S. R., Altincekic N., et al (2020) Oxford University Press (OUP) DOI: 10.1093/nar/gkaa1013	Nuclear magnetic resonance (NMR) experimental data deposited in COVID19-NMR project data Chemical shift data deposited in BMRB (multiple accession numbers, given in Table 1 in the article). data BioMagResBank
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
Serum-IgG responses to SARS-CoV-2 after mild and severe COVID-19 infection and analysis of IgG non-responders Marklund E., Leach S., Axelsson H., Nyström K., et al (2020) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0241104	Serum-IgG responses to SARS-CoV-2 after mild and severe COVID-19 infection. data Zenodo
Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries Bryant P., Elofsson A. (2020) PeerJ DOI: 10.7717/peerj.9879	Data required to reproduce the results. The data was largely produced using Google mobility data. data GitHub Analysis code required for modelliing (primarily using R). code GitHub
Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic Ling J., Hickman R. A., Li J., Lu X., et al (2020) MDPI AG DOI: 10.3390/v12091026	Supplementary materials include information about phylogenetic models, mutational profiles, and spatio-temporal appearance of each variant. 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
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
Probabilistic approaches for classifying highly variable anti-SARS-CoV-2 antibody responses Dopico X. C., Hanke L., Sheward D. J., Muschiol S., et al (2020) Cold Spring Harbor Laboratory DOI: 10.1101/2020.07.17.20155937	Code for discriminative bayesian seroprevalence. code GitHub Data for discriminative bayesian seroprevalence. data GitHub Code used in analysis of seroprevalence data. code GitHub Seroprevalence data. data GitHub
Neurochemical evidence of astrocytic and neuronal injury commonly found in COVID-19 Kanberg N., Ashton N. J., Andersson L., Yilmaz A., et al (2020) Ovid Technologies (Wolters Kluwer Health) DOI: 10.1212/WNL.0000000000010111	Data cannot be publicly shared, but applications can be made for access to anonymised data. data
Hyperreninemia and low total body water may contribute to acute kidney injury in COVID-19 patients in intensive care Hultström M., von Seth M., Frithiof R. (2020) Ovid Technologies (Wolters Kluwer Health) DOI: 10.1097/HJH.0000000000002531	Biochemistry of patients ordered by days after intensive care admission (n = 9), included in the article. data