Predicting protein secondary structure

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• Introduction
• The Golem dataset
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Introduction to secondary structure prediction

[Muggleton S., King R.D., and Sternberg M.J.E. (1992)]. The task is to learn rules to identify whether a position in a protein is in an alpha-helix. Points of relevance are:

• Each amino acid is denoted by a lower case character. There are 20 such amino acids.
• Positive examples state which positions of chosen proteins are in an alpha-helix. Negative examples state the positions that are not in an alpha-helix.
• The following background knowledge is provided:
• position(A,B,C). Residue of protein A at position B is C.
• octf(A,B,C,D,E,F,G,H,I). Arithmetic information that allows indexing groups of nine adjacent positions in a protein. Basically says positions A--I occur in sequence.
• alpha_triplet(A,B,C). Arithmetic information that allows indexing groups of three adjacent positions in a protein.
• alpha_pair(A,B). Arithmetic information that allows indexing a pair of adjacent positions in a protein.
• alpha_pair4(A,B). Arithmetic information that allows indexing a pair of positions separated by 4 positions in a protein.
• Physical and chemical properties of individual residues are described by unary predicates. These properties include hydrophobicity, hydrophilicity, charge, size, polarity, whether a residue is aliphatic or aromatic, whether it is a hydrogen donor or acceptor etc.
• Sizes, hydrophobicities, polarities etc., are represented by constants such as polar0 and polar1.
• Relations between the constants (less_than(polar0,polar1)) is also provided as background knowledge.

The Golem dataset

Bibliography