Help:
What are the various ID types?
1. AlphaFold Accessions: These accessions can be mapped directly
from UniProtKB Accessions to download structural coordinate files from AlphaFold Database.
2. UniProt Accessions: These are 6 or 10 alphanumerical character
long stable identifiers for UniProtKB entries.
They can be directly searched AlphaFold Structure Database. Click here to know more.
3. RefSeq Accessions: The NCBI Reference Sequence (RefSeq) project
provides non-redundant curated data of sequence records and
related information for numerous organisms, and provides a baseline for medical, functional, and
comparative studies. A RefSeq record can be identified by its distinct
accession number format that begins with two characters followed by an underscore (e.g., WP_). The
prefixes of these accessions are of various types. Click here to know
more.
4. Locus Tags: Locus_tags are identifiers that are systematically
applied to every protein coding and non-coding gene in a genome. Their prefixes are unique to every
organism and
there is only one locus_tag associated with one gene. The locus_tag prefix can contain only
alpha-numeric characters and it must be at least 3 characters long. Click here to know
more.
5. Old Locus Tags: The old locus tags were used prior to the
Prokaryotic Genome Annotation Pipeline (PGAP) re-annotation and the locus tags are the newer annotation.
On the current RefSeq bacterial genome record, the /old_locus_tag qualifier is still annotated. Click here
to know more.
6. TaxIDs: Each NCBI Taxonomy entry or TaxNode is assigned a public
stable, unique numerical identifier-the taxonomy identifier (TaxId)-which is shared by all names for a
specific TaxNode.
Click here to know
more.
Sample Inputs and Outputs:
If the input is AlphaFold Acessions or UniProt Accessions, the respective AlphaFold prediction will be downloaded. However, it is possible that some UniProt accessions will not have AlphaFold predicted structures, so no files will be downloaded for such cases.
| AlphaFold IDs |
|---|
| AF-Q9ULZ0-F1 |
| AF-Q8R143-F1 |
| AF-Q9LU47-F1 |
| AF-P05453-F1 |
| AF-Q7WTR3-F1 |
or
| UniProt Accessions |
|---|
| Q9ULZ0 |
| Q8R143 |
| Q9LU47 |
| P05453 |
| Q7WTR3 |
| Structure files downloaded |
|---|
| AF-Q9ULZ0-F1.pdb, AF-Q9ULZ0-F1.cif, AF-Q9ULZ0-F1_error.json |
| AF-Q8R143-F1.pdb, AF-Q8R143-F1.cif, AF-Q8R143-F1_error.json |
| AF-Q9LU47-F1.pdb, AF-Q9LU47-F1.cif, AF-Q9LU47-F1_error.json |
| AF-P05453-F1.pdb, AF-P05453-F1.cif, AF-P05453-F1_error.json |
| AF-Q7WTR3-F1.pdb, AF-Q7WTR3-F1.cif, AF-Q7WTR3-F1_error.json |
For RefSeq identifiers as the input, they could map either to single or multiple species such as example 1 and 3 in the table below. In cases when no structure file is downloaded, the reason could be that there is no corresponding UniProt Accession (example 2) or no predicted structure (example 4).
| RefSeq Protein IDs |
|---|
| NP_666037.1 |
| WP_296409975.1 |
| WP_004157415.1 |
| NP_056986.2 |
| Mapped UniProt Accession | Structure files downloaded |
|---|---|
| Q8R143 | AF-Q8R143-F1.pdb, AF-Q8R143-F1.cif, AF-Q8R143-F1_error.json |
| Not found | No files downloaded |
| A0A831EQJ9 Q7WTR3 D4I2C8 |
The files corresponding to all 3 UniProt accessions will be downloaded |
| O95071 | No predicted structures for this accession are available on AlphaFoldDB - No files downloaded |
For old locus tags as the input, they are mapped to the corresponding UniProt accession. In cases when no structure file is downloaded, the reason could be that there is no corresponding UniProt Accession (example 2, 4) or no predicted structure (example 3).
| Old Locus Tags |
|---|
| GVO57_04600 |
| L3078_27850 |
| CL52_18575 |
| LN051_09145 |
| Organism Name | Locus Tag | Old locus Tag | UniProt Accession | Files Downloaded |
|---|---|---|---|---|
| Sphingomonas changnyeongensis | GVO57_RS04600 | GVO57_04600 | A0A7Z2NV19 | AF-A0A7Z2NV19-F1.pdb, AF-A0A7Z2NV19-F1.cif, AF-A0A7Z2NV19-F1.bcif, AF-A0A7Z2NV19-F1_error.json |
| Streptomyces deccanensis | L3078_RS27850 | L3078_27850 | Not found | No files downloaded |
| Stutzerimonas balearica DSM 6083 | CL52_RS18275 | CL52_18575 | A0A8D3Y4T1 | No predicted structures for this accession are available on AlphaFoldDB - No files downloaded |
| Staphylococcus ratti strain CCM 9025 | LN051_RS09145 | LN051_09145 | Not found | No files downloaded |
For locus tags as the input, they are first mapped to old locus tags and these old locus tags are then mapped to UniProt accessions. This is done because the old locus tags have a one-to-one association with UniProt accessions. No structure file is downloaded, when a corresponding UniProt accession (example 2) or predicted structure (example 4) is not found.
| Locus Tags |
|---|
| GVO57_RS04600 |
| L3078_RS27850 |
| CL52_RS18275 |
| J0917_RS17640 |
| Organism Name | Locus Tag | Old locus Tag | UniProt Accession | Files Downloaded |
|---|---|---|---|---|
| Sphingomonas changnyeongensis | GVO57_RS04600 | GVO57_04600 | A0A7Z2NV19 | AF-A0A7Z2NV19-F1.pdb, AF-A0A7Z2NV19-F1.cif, AF-A0A7Z2NV19-F1.bcif, AF-A0A7Z2NV19-F1_error.json |
| Streptomyces deccanensis | L3078_RS27850 | L3078_27850 | Not found | No files downloaded |
| Stutzerimonas balearica DSM 6083 | CL52_RS18275 | A0A8D3Y4T1 | A0A8D3Y4T1 | No predicted structures for this accession are available on AlphaFoldDB - No files downloaded |
| Streptomyces nodosus | J0917_RS17640 | Not found | Not found | No files downloaded |
For NCBI TaxIDs as input, the structure files will be downloaded for all available AlphaFold predictions of proteins in that organism.
| Taxonomy IDs | Organism Name |
|---|---|
| 387662 | Candidatus Carsonella ruddii PV |
| Mapped UniProt Accessions for all proteins | Structure Files downloaded |
|---|---|
| Download mapped UniProt Accessions and details of all proteins in organism | Every protein whose structure files are available on AlphaFoldDB - will be downloaded |
API:
This service allows you download structures programatically on your terminal.
Template URL for single accession as input:
https://project.iith.ac.in/sharmaglab/alphafoldextractor/api/<id-type>/<id>
Template URL for multiple accessions as input:
https://project.iith.ac.in/sharmaglab/alphafoldextractor/api/<id-type>
<id-type>: oldlocustag / locustag / uniprot / alphafold / refseq / taxonomy
For multiple accessions, only ids and optionally format are accepted in request body.
format deafaults to 'pdb'.
ids : Comma seperated values. Spaces and '_' are tolerated. Unsupported symbols are converted to '_'.
format : [pdb] / cif / bcif / pae / all
Examples:
Single accession as input:
curl -JL https://project.iith.ac.in/sharmaglab/alphafoldextractor/api/oldlocustag/MXAN_1028 > structures.zip
wget --output-document=structures.zip https://project.iith.ac.in/sharmaglab/alphafoldextractor/api/oldlocustag/MXAN_1028
Multiple accessions as input:
curl -OJL -d "ids=MXAN_1028,GVO57_04600" https://project.iith.ac.in/sharmaglab/alphafoldextractor/api/oldlocustag
curl -JL -d "ids=MXAN_1028,GVO57_04600&&format=bcif" https://project.iith.ac.in/sharmaglab/alphafoldextractor/api/oldlocustag > MXAN_1028.zip
curl -JL -d "ids=MXAN_1028,GVO57_04600" -d "format=bcif" https://project.iith.ac.in/sharmaglab/alphafoldextractor/api/oldlocustag > MXAN_1028.zip
wget --post-data="ids=MXAN_1028,GVO57_04600" --content-disposition --trust-server-names https://project.iith.ac.in/sharmaglab/alphafoldextractor/api/oldlocustag
wget --post-data="ids=MXAN_1028&format=bcif" --output-document=MXAN_1028.zip https://project.iith.ac.in/sharmaglab/alphafoldextractor/api/oldlocustag