Add files using upload-large-folder tool

.gitattributes

@@ -58,3 +58,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+latest/msa_depths.csv filter=lfs diff=lfs merge=lfs -text

CHANGELOG.txt

@@ -0,0 +1,107 @@
+# AlphaFold Protein Structure Database Changelog
+
+## 2025-09-15
+* Updated to UniProt 2025_03.
+* Added 40,054 isoform sequences together with corresponding metadata.
+* Added new metadata fields to all sequences: authorNames, groupName,
+  proteinFullNames, taxonomicClassification, keywords, functions,
+  catalyticActivities.
+* Added Multiple Sequence Alignment (MSA) in the A3M format to all structures in
+  the database. This MSA was used as the input to the AlphaFold 2 model. This is
+  accompanied by msa_depths.csv which lists the MSA depth for each entry.
+* 241,070,489 structures
+* Differences in the number of proteins since v4:
+  * Added: 65,711,653 (including isoforms)
+  * Removed: 39,324,993
+  * Changed: 276,539
+  * Unchanged: 175,082,297
+
+
+### Changes
+* CIF: Occupancy now uses 2 decimal digits instead of 1.
+* CIF: Fixed global pLDDT `_ma_qa_metric_global.metric_value` to be computed as
+  a per-residue average, not per-atom.
+* CIF: `_citation_author.citation_id` now uses "primary" instead of "1".
+
+## 2022-11-01
+* Improved prediction accuracy of about 4.4% of predictions
+* 214,686,924 structures
+
+### Changes
+* CIF: `_citation.id` now uses `primary` instead of `1`.
+* Structures with consecutive CA-CA distance > 10 A are now filtered out.
+* The list of 9,203,041 accessions with updated coordinates in this release is
+  in `v4/v4_updated_accessions.txt`.
+* A sharded tar file with structures with updated coordinates in this release is
+  in `v4/updated_entries/v4_updated_entries-*.tar`. There are 921 shards
+  (from 0 to 920), each with at most 10,000 structures.
+
+## 2022-07-28
+* Added UniProt 2021_04
+* All CIF files are now ModelCIF-compliant
+* New PAE format that is about 4x smaller than the old one
+* 214,687,406 structures
+
+### Changes
+* CIF: Added support for templates (added `_ma_template_ref_db_details`,
+  `_ma_template_details`, `_ma_template_trans_matrix`, updated `_ma_data`).
+* CIF: Added `_pdbx_poly_seq_scheme.pdb_mon_id`, set to the same value as
+  `_pdbx_poly_seq_scheme.mon_id`.
+* CIF: Updated `_database_2.database_id` from `AF` to `AlphaFoldDB`
+  (new standardized value).
+* CIF: Updated `_ma_qa_metric.type` from `other` to `pLDDT` (new standardized
+  value).
+* CIF: Moved the legal disclaimer from `_ma_data.content_type_other_details` to
+  `_pdbx_data_usage` and added link to the license file.
+* CIF: Fixed `_ma_qa_metric_local.ordinal_id`, now going from 1 to `num_res`
+  instead of having constant value of 1.
+* CIF: Fixed `_pdbx_audit_revision_details`, now containing the full revision
+  history instead of just the last revision.
+* CIF: Added the `_ma_protocol_step` table.
+* CIF: `_audit_conform.dict_name` is now `mmcif_ma.dic` (previously
+  `mmcif_af.dic`).
+* CIF: `_audit_conform.dict_version` is now `1.3.9` (previously `1.0.2`).
+* CIF: Updated `_audit_conform.dict_location` to
+  `https://raw.githubusercontent.com/ihmwg/ModelCIF/master/dist/mmcif_ma.dic`.
+* PAE: New format that removes redundant `residue1` and `residue2` fields,
+  renames the `distance` field to `predicted_aligned_error` and stores the PAE
+  values rounded to the closest integer in a 2D matrix.
+* FTP: Renamed accession_ids.txt to accession_ids.csv.
+* FTP: The FASTA file now includes protein name, UniProt accession, UniProt
+  identifier, organism name, organism identifier, and gene name (if known).
+
+## 2022-01-27
+* Added Global Health Organisms
+* 995,411 structures
+
+### Changes
+* No format changes
+
+## 2021-12-09
+* Added Swiss-Prot
+* 804,872 structures
+
+### Changes
+* CIF: Added the `_pdbx_poly_seq_scheme` table.
+* CIF: DSSP now writes correct `beg_auth_seq_id` and `end_auth_seq_id`.
+* CIF: Updated Nature paper citation information.
+* CIF: Changed the model name from "AlphaFold model" to
+  "AlphaFold Monomer v2.0 model".
+* CIF: Updated the `_af_target_ref_db_details` table to match the ModelCIF
+  specification.
+* CIF: Updated `_audit_conform.dict_location` to point to the AFDB-specific
+  dictionary.
+* CIF: Added missing field `_struct_ref.pdbx_align_end`.
+* PDB: Fixed the `CRYST1` record to set also `Z = 1`.
+* PDB: Models are now indexed from 1 instead of from 0.
+* PDB: Updated Nature paper citation information.
+* PDB: Changed the model in TITLE from "ALPHAFOLD V2.0" to
+  "ALPHAFOLD MONOMER V2.0".
+* PAE: Colour normalization now has the same min (0.0) and max (31.75) for all
+  structures.
+* FTP: archives now contain version suffix which is set based on the maximum
+  version of any file in an archive.
+
+## 2021-07-22
+* Initial release of 21 model organisms
+* 365,198 structures

README.txt

@@ -0,0 +1,97 @@
+ALPHAFOLD DATABASE FTP README
+
+This document describes the types of files available from the AlphaFold DB FTP
+area at http://ftp.ebi.ac.uk/pub/databases/alphafold/.
+
+1.) download_metadata.json
+This file contains a list of all the archive files available for bulk download.
+The file is in JSON format and contains a list of objects with the following
+fields:
+
+* archive_name: The name of the archive file,
+  e.g. "UP000006548_3702_ARATH_v2.tar", string, required
+* num_predicted_structures: The count of predicted structures in the archive,
+  e.g. 27434, number, required
+* size_bytes: The size of the archive file in bytes,
+  e.g. 3855707136, number, required
+* type: The type/category of the archive file, e.g. "proteome", string, required
+* species: The scientific name of the corresponding species,
+  e.g. "Homo sapiens", string, optional
+* common_name: A common name of the corresponding species,
+  e.g. "Human", string, optional
+* latin_common_name: Indicates if the common name is in Latin,
+  e.g. true, boolean, optional
+* reference_proteome: The identifier of the reference proteome,
+  e.g. "UP000006548", string, optional
+* label: A label for the archive file,
+  e.g. "Swiss-Prot (CIF files)", string, optional
+
+2.) accession_ids.csv
+This file contains a list of all the UniProt accessions that have predictions in
+the current database version of AlphaFold DB. The file is in CSV format and
+includes the following columns, separated by a comma:
+
+* UniProt accession, e.g. A8H2R3
+* First residue index (UniProt numbering), e.g. 1
+* Last residue index (UniProt numbering), e.g. 199
+* AlphaFold DB identifier, e.g. AF-A8H2R3-F1
+* Latest version, e.g. 2
+
+3.) msa_depths.csv
+This file contains Multiple Sequence Alignment (MSA) depths for every entry in
+the database. These depths correspond to the MSA files that have been given as
+an input to AlphaFold to generate the structure prediction. The file is in CSV
+format and includes the following columns, separated by a comma:
+
+* AFDB accession, e.g. AF-A8H2R3-F1
+* Multiple Sequence Alignment (MSA) depth, e.g. 1989. This is the number of
+  sequences in the MSA file.
+
+4.) sequences.fasta
+This file contains sequences for all proteins in the current database version in
+FASTA format.
+
+The format for the identifier row is:
+>AFDB:UniqueIdentifier ProteinName UA=UniprotAccession UI=UniprotIdentifier
+ OS=OrganismName OX=OrganismIdentifier [GN=GeneName]
+For example:
+>AFDB:AF-Q5VSL9-F1 Striatin-interacting protein 1 UA=Q5VSL9 UI=Q5VSL9
+ OS=Homo Sapiens OX=9606 GN=STRIP1
+
+The fields in the identifier row match UniProt fields described in
+https://www.uniprot.org/help/fasta-headers. The GN=GeneName field is optional
+and provided only if known.
+
+The sequence row contains the corresponding amino acid sequence. Each sequence
+is on a single line, i.e. there is no wrapping.
+
+5.) *.tar
+These files are organised into several folders. The folder “latest” contains the
+latest version of the archive files, while v* folders (e.g. v1, v2, etc.) have
+the corresponding versions of the archive files.
+
+The archive files are TAR archives of GZIP compressed files for atomic
+coordinate data in PDB and mmCIF formats.
+
+6.) diffs.ndjson.gz
+This file lists entries that were added, removed, or changed in the current
+database version. The file is newline-delimited JSON (NDJSON) compressed with 
+gzip. Each line is a single record with the following fields:
+
+id: AlphaFold DB identifier, e.g. "AF-Q5VSL9-F1", string, required
+
+status: Change type, one of "ADDED", "REMOVED", "CHANGED", string, required
+
+ref_len: Sequence length in the previous release, number, optional (only 
+for "CHANGED")
+
+cmp_len: Sequence length in the current release, number, optional (only 
+for "CHANGED")
+
+Example (one record per line):
+{"id":"AF-A0A016SDI7-F1","status":"ADDED"}
+{"id":"AF-A0A009DWB1-F1","status":"REMOVED"}
+{"id":"AF-A0A017SPL2-F1","status":"CHANGED","ref_len":408,"cmp_len":409}
+
+Note: This file is the canonical per-release diff. It can be streamed and 
+filtered with standard tools (e.g. zcat, jq).

download_metadata.json

@@ -0,0 +1 @@
+[{"archive_name": "UP000006548_3702_ARATH_v6.tar", "species": "Arabidopsis thaliana", "common_name": "Arabidopsis", "latin_common_name": true, "reference_proteome": "UP000006548", "num_predicted_structures": 27402, "size_bytes": 3877400576, "type": "proteome"}, {"archive_name": "UP000001940_6239_CAEEL_v6.tar", "species": "Caenorhabditis elegans", "common_name": "Nematode worm", "latin_common_name": false, "reference_proteome": "UP000001940", "num_predicted_structures": 19700, "size_bytes": 2777489920, "type": "proteome"}, {"archive_name": "UP000000559_237561_CANAL_v6.tar", "species": "Candida albicans", "common_name": "C. albicans", "latin_common_name": true, "reference_proteome": "UP000000559", "num_predicted_structures": 5973, "size_bytes": 1028541440, "type": "proteome"}, {"archive_name": "UP000000437_7955_DANRE_v6.tar", "species": "Danio rerio", "common_name": "Zebrafish", "latin_common_name": false, "reference_proteome": "UP000000437", "num_predicted_structures": 26290, "size_bytes": 4979466752, "type": "proteome"}, {"archive_name": "UP000002195_44689_DICDI_v6.tar", "species": "Dictyostelium discoideum", "common_name": "Dictyostelium", "latin_common_name": true, "reference_proteome": "UP000002195", "num_predicted_structures": 12612, "size_bytes": 2292386816, "type": "proteome"}, {"archive_name": "UP000000803_7227_DROME_v6.tar", "species": "Drosophila melanogaster", "common_name": "Fruit fly", "latin_common_name": false, "reference_proteome": "UP000000803", "num_predicted_structures": 13461, "size_bytes": 2319755776, "type": "proteome"}, {"archive_name": "UP000000625_83333_ECOLI_v6.tar", "species": "Escherichia coli", "common_name": "E. coli", "latin_common_name": true, "reference_proteome": "UP000000625", "num_predicted_structures": 4370, "size_bytes": 477871104, "type": "proteome"}, {"archive_name": "UP000008827_3847_SOYBN_v6.tar", "species": "Glycine max", "common_name": "Soybean", "latin_common_name": false, "reference_proteome": "UP000008827", "num_predicted_structures": 55796, "size_bytes": 7616606720, "type": "proteome"}, {"archive_name": "UP000005640_9606_HUMAN_v6.tar", "species": "Homo sapiens", "common_name": "Human", "latin_common_name": false, "reference_proteome": "UP000005640", "num_predicted_structures": 23586, "size_bytes": 5177506304, "type": "proteome"}, {"archive_name": "UP000000805_243232_METJA_v6.tar", "species": "Methanocaldococcus jannaschii", "common_name": "M. jannaschii", "latin_common_name": true, "reference_proteome": "UP000000805", "num_predicted_structures": 1773, "size_bytes": 181713920, "type": "proteome"}, {"archive_name": "UP000000589_10090_MOUSE_v6.tar", "species": "Mus musculus", "common_name": "Mouse", "latin_common_name": false, "reference_proteome": "UP000000589", "num_predicted_structures": 21452, "size_bytes": 3782078976, "type": "proteome"}, {"archive_name": "UP000059680_39947_ORYSJ_v6.tar", "species": "Oryza sativa", "common_name": "Asian rice", "latin_common_name": false, "reference_proteome": "UP000059680", "num_predicted_structures": 43645, "size_bytes": 4723294720, "type": "proteome"}, {"archive_name": "UP000002494_10116_RAT_v6.tar", "species": "Rattus norvegicus", "common_name": "Rat", "latin_common_name": false, "reference_proteome": "UP000002494", "num_predicted_structures": 22152, "size_bytes": 3776509440, "type": "proteome"}, {"archive_name": "UP000002311_559292_YEAST_v6.tar", "species": "Saccharomyces cerevisiae", "common_name": "Budding yeast", "latin_common_name": false, "reference_proteome": "UP000002311", "num_predicted_structures": 6055, "size_bytes": 1024019456, "type": "proteome"}, {"archive_name": "UP000002485_284812_SCHPO_v6.tar", "species": "Schizosaccharomyces pombe", "common_name": "Fission yeast", "latin_common_name": false, "reference_proteome": "UP000002485", "num_predicted_structures": 5196, "size_bytes": 840982016, "type": "proteome"}, {"archive_name": "UP000007305_4577_MAIZE_v6.tar", "species": "Zea mays", "common_name": 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