Protein
Alpha-helix prediction in protein sequences, encoded as ILP problems. The task is to predict which positions in a protein sequence form part of an alpha-helix, based on the amino acid identity and physico-chemical properties at each position.
Tasks: 1 (single task in train/)
Head relation: alpha(Protein, Index) — position Index in protein Protein is part of an alpha-helix.
Background relations:
| Relation | Arity | Description |
|---|---|---|
position(Protein, Index, AminoAcid) |
3 | Position Index in protein Protein has amino acid AminoAcid |
alpha_pair3(I1, I2) |
2 | Indices I1 and I2 are 3 positions apart (used to detect helix periodicity) |
alpha_triplet(I1, I2, I3) |
3 | Indices I1, I2, I3 form a triplet pattern |
octf(I1,...,I9) |
9 | Nine consecutive indices forming an octamer window |
lth(A1, A2) |
2 | Amino acid A1 is less than A2 in hydrophobicity |
ltv(A1, A2) |
2 | Amino acid A1 is less than A2 in volume |
aliphatic(A) |
1 | Amino acid A is aliphatic |
aromatic(A) |
1 | Amino acid A is aromatic |
polar(A) |
1 | Amino acid A is polar |
hydrophobic(A) |
1 | Amino acid A is hydrophobic |
hydrophilic(A) |
1 | Amino acid A is hydrophilic |
very_hydrophobic(A) |
1 | Amino acid A is very hydrophobic |
small(A) |
1 | Amino acid A has a small side chain |
tiny(A) |
1 | Amino acid A has a tiny side chain |
large(A) |
1 | Amino acid A has a large side chain |
positive(A) |
1 | Amino acid A has a positively charged side chain |
negative(A) |
1 | Amino acid A has a negatively charged side chain |
neutral(A) |
1 | Amino acid A is charge-neutral |
hydro_b_acc(A) |
1 | Amino acid A is a hydrogen-bond acceptor |
hydro_b_don(A) |
1 | Amino acid A is a hydrogen-bond donor |
aromatic_or_very_hydrophobic(A) |
1 | Amino acid A is aromatic or very hydrophobic |
ar_or_al_or_m(A) |
1 | Amino acid A is aromatic, aliphatic, or methionine |
small_or_polar(A) |
1 | Amino acid A is small or polar |
not_aromatic(A) |
1 | Amino acid A is not aromatic |
not_<aa>(A) |
1 | Type-constant: A is not a specific amino acid (one relation per residue letter) |
Task statistics
| task_name | num_bk_facts | num_bk_relations | num_pos_examples | num_neg_examples |
|---|---|---|---|---|
protein |
4027 | 44 | 848 | 764 |
Source: IC London ILP Dataset Collection. Retrieved from https://www.doc.ic.ac.uk/~shm/Datasets/proteins/