| name | protein_property_prediction |
| description | Physicochemical properties, surface/SS features, and finetuned protein/residue function prediction. Use when the user asks for solubility, optimal temperature, activity/binding/conserved sites, RSA/SASA/secondary structure, or property tables from FASTA/PDB. Do NOT use for zero-shot mutation ranking (zero_shot_mutation_workflow) or custom model training (train tools / future finetune workflow). |
| license | Apache-2.0 |
| metadata | {"version":"1.0","skill-author":"VenusFactory2"} |
Protein Property & Function Prediction
Overview
Orchestrates VenusFactory predict tools: FASTA physicochemical features, PDB RSA/SASA/SS, and finetuned sequence-level / residue-level function heads (Ankh / ESM2 / ProtT5 adapters under ckpt/).
Project Tools (VenusFactory2)
| Tool | Args | When |
|---|
| calculate_physchem_from_fasta | fasta_file, optional out_dir | Length, MW, pI, gravy, etc. |
| calculate_rsa_from_pdb | pdb_file, chain_id | Relative solvent accessibility |
| calculate_sasa_from_pdb | pdb_file | Absolute SASA |
| calculate_ss_from_pdb | pdb_file, chain_id | Secondary structure |
| predict_protein_function | fasta_file, task, model_name | Solubility, Optimal Temperature, … |
| predict_residue_function | fasta_file, task, model_name | Activity / Binding / Conserved Site / Motif |
| predict_structure_esmfold | sequence | Need PDB before RSA/SASA/SS |
Workflow
Properties from sequence
calculate_physchem_from_fasta- Optional
predict_protein_function with an explicit task matching platform dataset names.
Structure features
- Obtain PDB (
protein_structure_pipeline or user upload).
- Run
calculate_rsa_from_pdb / calculate_sasa_from_pdb / calculate_ss_from_pdb as needed.
Residue sites
predict_residue_function with task in {Activity Site, Binding Site, Conserved Site, Motif}.- Cross-check with InterPro (
interpro_domain_annotation) before proposing edits to catalytic residues.
Common mistakes
- Inventing
task names not present in platform constant.json / ckpt mapping.
- Running RSA tools on FASTA without a structure.
- Treating finetuned scores as wet-lab labels without reporting model/task.
