What is the Length Limit for AlphaFold?
The length limits for proteins available through the AlphaFold Database vary, depending on the source of the protein entries. These limits define the size range of pre-computed protein structures that users can access and download for their research and analysis.
Understanding AlphaFold Database Length Limits
When accessing pre-computed protein structures from the AlphaFold Database, it's important to be aware of both the minimum and maximum amino acid lengths supported. These parameters help users efficiently query and utilize the vast repository of predicted structures.
Minimum Length
All proteins included in the AlphaFold Database must meet a specific minimum length requirement.
- Minimum Length: 16 amino acids
Maximum Lengths
The upper limit for protein length differs based on the type of entry within the UniProt database, from which AlphaFold structures are derived:
- For Proteomes and Swiss-Prot (Reviewed Entries): Proteins originating from complete proteomes or those that have undergone extensive review in Swiss-Prot can be significantly longer.
- Maximum Length: 2,700 amino acids
- For the Rest of UniProt (Unreviewed Entries): Proteins from the broader UniProt database, particularly those that are not yet fully reviewed, have a more constrained maximum length.
- Maximum Length: 1,280 amino acids
Special Considerations for the Human Proteome
For researchers specifically interested in the human proteome, there's a particular access method that allows for handling even longer proteins than the standard maximums:
- When accessing the human proteome via FTP download, proteins exceeding the typical maximum lengths are included.
- These exceptionally long human proteins are segmented into fragments to comply with processing capabilities and database structures. This approach ensures that comprehensive data for the human proteome is available, even for very large proteins, by breaking them down into manageable parts.
Summary of AlphaFold Database Length Limits
To provide a clear overview, the table below summarizes the various length constraints for proteins accessible through the AlphaFold Database:
| Category | Minimum Length (Amino Acids) | Maximum Length (Amino Acids) | Notes |
|---|---|---|---|
| All Proteins | 16 | — | Universal minimum length for all entries in the AlphaFold Database. |
| Proteomes & Swiss-Prot (Reviewed) | 16 | 2,700 | Applies to fully reviewed and curated protein entries from complete proteomes. |
| Rest of UniProt (Unreviewed) | 16 | 1,280 | Applies to unreviewed or less curated protein entries from the broader UniProt database. |
| Human Proteome (via FTP download only) | 16 | (Varies) | Longer proteins are included but are segmented into fragments for download, allowing access to structures beyond the typical maximums. |
These limits are crucial for understanding the scope of available pre-computed protein structures and planning data retrieval strategies from the AlphaFold Database.
