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README.md
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## Usage Notes
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- The **internal index** (`idx`) is the key that ties together:
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- build training or evaluation sets for ligand–target or ligand–domain prediction,
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- separate high-confidence from ambiguous associations,
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- benchmark methods that infer protein targets from ligand similarity.
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---
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### 4. Organism-Specific Datasets
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ReverseLigQ integrates multiple organisms, each identified by an integer key.
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The files in this section provide organism-level ligand lists, protein descriptions, and Pfam-based protein families.
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Organism keys and corresponding species:
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| Key | Organism |
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|-----|----------|
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| 1 | *Bartonella bacilliformis* |
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| 2 | *Klebsiella pneumoniae* |
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| 3 | *Mycobacterium tuberculosis* |
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| 4 | *Trypanosoma cruzi* |
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| 5 | *Staphylococcus aureus* RF122 |
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| 6 | *Streptococcus uberis* 0140J |
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| 7 | *Enterococcus faecium* |
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| 8 | *Escherichia coli* MG1655 |
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| 9 | *Streptococcus agalactiae* NEM316 |
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| 10 | *Pseudomonas syringae* |
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| 11 | DENV (Dengue virus) |
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| 12 | SARS-CoV-2 |
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| 13 | *Homo sapiens* |
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#### Files:
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- **`ligand_lists.pkl`**
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Python dictionary containing the **list of ligands associated with each organism** included in the platform.
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Keys correspond to organism indices (1–13), and values are lists of ligand identifiers.
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- **`prot_descriptions.pkl`**
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Python dictionary containing **protein descriptions** (annotations, names, functional summaries, etc.) for each organism.
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Keys are the organism indices listed above.
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- **`fam_prot_dict.pkl`**
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Python dictionary mapping each organism to its **proteins grouped by Pfam families**.
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For each organism key, the value is another dictionary where:
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- keys are Pfam domain identifiers, and
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- values are lists of proteins belonging to that domain family.
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These files enable ReverseLigQ to perform organism-specific ligand searches, identify relevant targets, and reconstruct ligand–domain landscapes across diverse pathogens and host species.
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---
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## Usage Notes
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- The **internal index** (`idx`) is the key that ties together:
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- build training or evaluation sets for ligand–target or ligand–domain prediction,
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- separate high-confidence from ambiguous associations,
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- benchmark methods that infer protein targets from ligand similarity.
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- The organism-level dictionaries (`ligand_lists.pkl`, `prot_descriptions.pkl`, `fam_prot_dict.pkl`) support:
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- organism-specific prioritization of targets,
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- analyses of Pfam family distribution across species,
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- integration of ligand knowledge with genomic and proteomic data.
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---
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