Protein Module API Documentation

The Protein module provides functionality for working with protein sequences, structures, and AlphaFold2 predictions.

Core Functions

get_seq_from_gene_name	Get protein sequence for a given gene name.
get_seq_from_uniprot_id	Get protein sequence for a given UniProt ID.
get_lddt_from_gene_name	Get AlphaFold pLDDT scores for a given gene name.
get_lddt_from_uniprot_id	Get AlphaFold pLDDT scores for a given UniProt ID.
get_uniprot_from_gene_name	Get UniProt ID for a given gene name.

Protein Class

• Description: Base class for working with protein sequences and AlphaFold2 predictions.

• Key Methods:

  • plot_plddt(): Plots pLDDT scores with optional domain annotations.

  • plotly_plddt(): Interactive Plotly version of pLDDT plot.

  • get_domain_from_uniprot(): Gets domain information from UniProt.

UniProt API

UniProtAPI

A class to interact with UniProt API for protein-related data retrieval.

UniProtAPI

• Description: Class for interacting with the UniProt REST API.

• Key Methods:

  • get_uniprot_id(): Gets UniProt ID from gene name.

  • get_protein_sequence(): Gets protein sequence from UniProt ID.

  • get_domains(): Gets domain information for a protein.

  • get_protein_info(): Gets detailed protein information.

STRING Database API

get_string_network

• Description: Retrieve protein-protein interaction network data from the STRING database.

• Parameters:

  • identifiers: List of protein identifiers (gene symbols or STRING IDs).

  • species: Species name for the proteins (default: “human”).

  • network_type: Type of interaction network (“physical” or “functional”).

  • required_score: Minimum required interaction score (0-1000).

  • save_image: Path to save the network visualization image.

• Returns: DataFrame containing the interaction network data.

InterPro API

InterProAPI

• Description: A class to interact with the InterPro API for protein domain and feature data.

• Key Methods:

  • get_protein_entries(uniprot_id): Get all InterPro entries for a protein.

  • get_entry_info(entry_id): Get detailed information about an InterPro entry.

  • search_by_name(query, entry_type): Search InterPro entries by name/description.

  • get_domain_architecture(uniprot_id): Get the domain architecture of a protein.

  • get_protein_families(uniprot_id): Get protein family classifications.

  • get_protein_go_terms(uniprot_id): Get GO terms associated with protein’s InterPro entries.

AlphaFold2 Analysis

AFResult	AlphaFold result from a files
AFMonomer	An AFResult class for AF2 Monomer prediction
AFHomodimer	An AFResult class for AF2 Homodimer prediction
AFMultimer	An AFResult class for AF2 Multimer prediction
AFPairseg	Pass the base result directory name Gene1_Gene2.

AFResult

• Description: Base class for analyzing AlphaFold2 prediction results.

• Key Attributes:

  • plddt: Per-residue pLDDT confidence scores.

  • pae: Predicted Aligned Error matrix.

  • iptm: Interface TM-score.

  • ptm: Predicted TM-score.

AFPairseg

• Description: Class for analyzing AlphaFold2 predictions of protein segment pairs.

• Key Methods:

  • plot_plddt_gene1(): Plots pLDDT scores for first protein.

  • plot_plddt_gene2(): Plots pLDDT scores for second protein.

  • plot_score_heatmap(): Plots heatmap of interaction scores.

Data Management

Organism Mappings

# Map organism names to UniProt identifiers
organism_to_uniprot = {
    "human": "HUMAN_9606",
    "mouse": "MOUSE_10090",
    "rat": "RAT_10116",
    # ...
}

# Map UCSC genome builds to organisms
ucsc_to_organism = {
    "hg38": "human",
    "mm10": "mouse",
    "hg19": "human",
    # ...
}

Data Loading

The module implements lazy loading of protein data:

• UniProt sequences

• Gene name to UniProt ID mappings

• AlphaFold pLDDT scores

• UniProt XML schema

Data is downloaded automatically when first needed.