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Contents

1. Working directories
2. Protein Interaction/PPI
3. Drive5.com
4. AlphaFold Protein Structure Database
1. 4.1. Home
2. 4.2. Downloads
5. Protein Structure Prediction

Working directories

1
2
3

# Book of "Protein Structure Prediction"
i=/media/ht/ht_5T/Work/References/eBooks/Important_Protocols/Protein_Structure_Prediction.pdf; \
setsid okular ${i}

Protein Interaction/PPI

Drive5.com

USEARCH >
Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST.

MUSCLE >
Multiple sequence alignment. Faster and more accurate than CLUSTALW.

UPARSE >
OTU clustering for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures.

UCHIME >
Chimeric sequence detection.

PILER >
De novo genome repeat finder.

PILER-CR >
Detection of CRISPR repeats in bacterial genomes.

URMAP >> new
Ultra-fast read mapper.

PALS >
Whole-genome alignment.

PREFAB >
Protein Reference Alignment Database.

MSA benchmark collection >
Selected multiple alignment benchmarks in a standardized FASTA format.

AlphaFold Protein Structure Database

Home

Background

AlphaFold is an AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence. It regularly achieves accuracy competitive with experiment.

DeepMind and EMBL’s European Bioinformatics Institute (EMBL-EBI) have partnered to create AlphaFold DB to make these predictions freely available to the scientific community. The first release covered the human proteome and the proteomes of several other key organisms, while the second release added the majority of manually curated UniProt entries (Swiss-Prot). In 2022 we plan to expand the database to cover a large proportion of all catalogued proteins (the over 100 million in UniRef90).

Q8I3H7: May protect the malaria parasite against attack by the immune system. Mean pLDDT 85.57.

View protein

In CASP14, AlphaFold was the top-ranked protein structure prediction method by a large margin, producing predictions with high accuracy. While the system still has some limitations, the CASP results suggest AlphaFold has immediate potential to help us understand the structure of proteins and advance biological research.

Let us know how the AlphaFold Protein Structure Database has been useful in your research, or if you have any questions not covered in the FAQs, at alphafold@deepmind.com.

Q8W3K0: A potential plant disease resistance protein. Mean pLDDT 82.24.

View protein

Find out more

Methodology Human proteome predictions Downloads

About AlphaFold DB DeepMind EMBL-EBI

What’s next?

AlphaFold DB will continue to expand in the coming months, so if you can’t find what you’re looking for right now, please follow DeepMind and EMBL-EBI’s social channels for updates. In the meantime the AlphaFold source code and Colab notebook can be used to predict the structures of proteins not yet in AlphaFold DB. Both resources were recently updated to support multimer prediction.

License and attribution

All of the data provided is freely available for both academic and commercial use under Creative Commons Attribution 4.0 (CC-BY 4.0) license terms. If you use this resource, please cite the following papers:

Jumper, J et al. Highly accurate protein structure prediction with AlphaFold. Nature (2021).

Varadi, M et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Research (2021).

The structures provided in this resource are predictions with varying levels of confidence and should be interpreted carefully.

Downloads

AlphaFold DB currently provides predicted structures for the organisms listed below, as well as the majority of Swiss-Prot.

You can download a prediction for an individual UniProt accession by visiting the corresponding structure page (example: https://www.alphafold.ebi.ac.uk/entry/F4HVG8).

For downloading all predictions for a given species, use the download links below. Note that this option is only available on the desktop version of the site.

These uncompressed archive files (.tar) contain all the available compressed PDB and mmCIF files (.gz) for a reference proteome. In the case of proteins longer than 2700 amino acids (aa), AlphaFold provides 1400aa long, overlapping fragments. For example, Titin has predicted fragment structures named as Q8WZ42-F1 (residues 1–1400), Q8WZ42-F2 (residues 201–1600), etc. These fragments are currently only available in these proteome archive files, not on the website.

For downloading all predictions for all species, visit the FTP site: ftp://ftp.ebi.ac.uk/pub/databases/alphafold

Compressed prediction files for model organism proteomes:

Species

Common Name

Reference Proteome

Predicted Structures

Download

Arabidopsis thaliana

Arabidopsis

UP000006548

27,434

Download (3,678 MB)

Caenorhabditis elegans

Nematode worm

UP000001940

19,694

Download (2,626 MB)

Candida albicans

C. albicans

UP000000559

5,974

Download (974 MB)

Danio rerio

Zebrafish

UP000000437

24,664

Download (4,180 MB)

Dictyostelium discoideum

Dictyostelium

UP000002195

12,622

Download (2,171 MB)

Drosophila melanogaster

Fruit fly

UP000000803

13,458

Download (2,195 MB)

Escherichia coli

E. coli

UP000000625

4,363

Download (453 MB)

Glycine max

Soybean

UP000008827

55,799

Download (7,211 MB)

Homo sapiens

Human

UP000005640

23,391

Download (4,830 MB)

Methanocaldococcus jannaschii

M. jannaschii

UP000000805

1,773

Download (172 MB)

Mus musculus

Mouse

UP000000589

21,615

Download (3,581 MB)

Oryza sativa

Asian rice

UP000059680

43,649

Download (4,461 MB)

Rattus norvegicus

Rat

UP000002494

21,272

Download (3,437 MB)

Saccharomyces cerevisiae

Budding yeast

UP000002311

6,040

Download (969 MB)

Schizosaccharomyces pombe

Fission yeast

UP000002485

5,128

Download (783 MB)

Zea mays

Maize

UP000007305

39,299

Download (5,064 MB)

Compressed prediction files for global health proteomes:

Species

Common Name

Reference Proteome

Predicted Structures

Download

Ajellomyces capsulatus

9,199

Brugia malayi

8,743

Campylobacter jejuni

C. jejuni

UP000000799

1,620

Download (173 MB)

Cladophialophora carrionii

UP000094526

11,170

Download (1,716 MB)

Dracunculus medinensis

10,834

Enterococcus faecium

2,823

Fonsecaea pedrosoi

12,509

Haemophilus influenzae

H. influenzae

UP000000579

1,662

Download (173 MB)

Helicobacter pylori

H. pylori

UP000000429

1,538

Download (165 MB)

Klebsiella pneumoniae

K. pneumoniae

UP000007841

5,727

Download (554 MB)

Leishmania infantum

L. infantum

UP000008153

7,924

Download (1,496 MB)

Madurella mycetomatis

9,561

Mycobacterium leprae

1,602

Mycobacterium tuberculosis

M. tuberculosis

UP000001584

3,988

Download (425 MB)

Mycobacterium ulcerans

UP000020681

9,033

Download (575 MB)

Neisseria gonorrhoeae

N. gonorrhoeae

UP000000535

2,106

Download (194 MB)

Nocardia brasiliensis

8,372

Onchocerca volvulus

12,047

Paracoccidioides lutzii

UP000002059

8,794

Download (1,284 MB)

Plasmodium falciparum

P. falciparum

UP000001450

5,187

Download (1,142 MB)

Pseudomonas aeruginosa

P. aeruginosa

UP000002438

5,556

Download (608 MB)

Salmonella typhimurium

S. typhimurium

4,526

Schistosoma mansoni

13,865

Shigella dysenteriae

S. dysenteriae

3,893

Sporothrix schenckii

8,652

Staphylococcus aureus

S. aureus

UP000008816

2,888

Download (271 MB)

Streptococcus pneumoniae

S. pneumoniae

UP000000586

2,030

Download (201 MB)

Strongyloides stercoralis

12,613

Trichuris trichiura

9,564

Trypanosoma brucei

8,491

Trypanosoma cruzi

T. cruzi

19,036

Wuchereria bancrofti

12,721

Compressed prediction files for Swiss-Prot:

File type

Predicted Structures

Download

Swiss-Prot (CIF files)

542,380

Download (36,896 MB)

Swiss-Prot (PDB files)

542,380

Download (26,935 MB)

License and attribution

Data is available for academic and commercial use, under a CC-BY-4.0 license.

EMBL-EBI expects attribution (e.g. in publications, services or products) for any of its online services, databases or software in accordance with good scientific practice.

If you make use of an AlphaFold prediction, please cite the following papers:
Jumper, J et al. Highly accurate protein structure prediction with AlphaFold. Nature (2021).Varadi, M et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Research (2021).

Feedback

If you want to share feedback on an AlphaFold structure prediction please contact alphafold@deepmind.com. If you have feedback on the website or experience any bugs please contact afdbhelp@ebi.ac.uk.

Disclaimer

The AlphaFold Data and other information provided on this site is for theoretical modelling only, caution should be exercised in its use. It is provided ‘as-is’ without any warranty of any kind, whether expressed or implied. For clarity, no warranty is given that use of the information shall not infringe the rights of any third party. The information is not intended to be a substitute for professional medical advice, diagnosis, or treatment, and does not constitute medical or other professional advice.

Use of the AlphaFold Protein Structure Database is subject to EMBL-EBI Terms of Use.

Protein Structure Prediction