uniprot_protparams

Protein-level sequence property dataset for UniProtKB entries. length and mass are UniProt-reported; the other properties are calculated with Biopython's ProteinAnalysis. Select one property per scalar regression run with steps.prepare.label_column.

Source and preprocessing

• UniProt REST API: https://rest.uniprot.org/uniprotkb/stream
• Card generated (UTC): 2026-10-07
• UniProt query: (organism_id:9606) AND (reviewed:true)
• Organism Taxonomy ID: 9606.
• Review status: reviewed (reviewed = Swiss-Prot, unreviewed = TrEMBL, all = both).
• No filter is applied based on UniProt-reported protein length.
• Ambiguous residues are normalized for analysis as U->C, O->L, B->N, Z->Q, J->L, and X->G; the original sequence is retained.
• Property columns: length, mass, percent_a, percent_c, percent_d, percent_e, percent_f, percent_g, percent_h, percent_i, percent_k, percent_l, percent_m, percent_n, percent_p, percent_q, percent_r, percent_s, percent_t, percent_v, percent_w, percent_y, fraction_helix_aas, fraction_turn_aas, fraction_sheet_aas, instability_index, gravy, isoelectric_point, charge_at_ph4_7, charge_at_ph7_2, charge_at_ph8.
• Properties are sequence-derived estimates, not experimental measurements.
• No maximum sequence-length filter was applied.

Splits

MMseqs2 cluster holdout using split fractions {'train': 0.8, 'validation': 0.1, 'test': 0.1}. Seed: 1957723. Clustering settings:

• MMseqs workflow: easy-cluster
• Minimum sequence identity (--min-seq-id): 0.3
• Minimum coverage (-c): 0.8
• Coverage mode (--cov-mode): 1
• Threads: 1
• Other MMseqs2 options use MMseqs2 defaults.

When create_split_subsets is enabled, pooled random, length-stratified, and hold-cluster-out subsets are also included. Hold-cluster-out subsets require enough MMseqs clusters to populate all three roles.

• test: 2035 rows
• test_cluster: 2035 rows
• test_random: 2035 rows
• test_stratified: 2035 rows
• train: 16283 rows
• train_cluster: 16283 rows
• train_random: 16283 rows
• train_stratified: 16283 rows
• validation: 2035 rows
• validation_cluster: 2035 rows
• validation_random: 2035 rows
• validation_stratified: 2035 rows

stats.json contains row counts, columns, and sequence-length metrics.