\documentstyle[12pt,a4]{article}
\input{epsf}

\begin{document}
\section*{Predicting protein secondary structure}
A protein is basically a string of amino acids (or {\bf residues}).
Predicting the three-dimensional shape of proteins
from their amino acid sequence is widely believed
to be one of the hardest unsolved problems in
molecular biology. It is also of considerable
interest to pharmaceutical companies since
shape generally determines the function of
a protein. This is what a protein looks like:
\begin{figure*}[htb]
% \epsfxsize=\textwidth
\epsfxsize=3.0in
\epsfysize=3.0in
\centerline{\epsfbox{prot.eps}}
\end{figure*}

The sequence of amino acids is called
the {\bf primary structure} of the protein. Spatially, 
the amino acids are arranged in different patterns (spirals,
turns, flat sections etc.). The interest here is in one particular
shape (or {\bf secondary structure}), namely when the protein
shape is a helical one. This shape is called an $\alpha$-helix.

The data here is from the {\em Golem \/} \cite{mugfeng:golem} experiments
reported in \cite{mugking:proteins}. 
The task is to learn rules to identify whether a position in a protein
is in an $\alpha$-helix. Points of relevance are:
\begin{itemize}
\item Each amino acid is denoted by a lower case character. There are
	20 such amino acids.
\item 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.
\item The following background knowledge is provided:
\begin{itemize}
\item {\bf position(A,B,C)}. Residue of protein A at position B is C.
\item {\bf octf(A,B,C,D,E,F,G,H,I)}. Arithmetic information the allows indexing
groups of nine adjacent positions in a protein. Basically says positions A--I occur
in sequence.
\item {\bf alpha\_triplet(A,B,C)}. Arithmetic information the allows indexing
groups of three adjacent positions in a protein.
\item {\bf  alpha\_pair(A,B)}. Arithmetic information the allows indexing
a pair of adjacent positions in a protein.
\item {\bf  alpha\_pair4(A,B)}. Arithmetic information the allows indexing
a pair of positions separated by 4 positions in a protein.
\item 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 donator or acceptor etc.
\item Sizes, hydrophobicities, polarities etc., are represented by constants
	(for example, polar0, polar1 etc.).
\item Relations between the constants (less\_than(polar0,polar1)) is
	also provided as background knowledge.
\end{itemize}
\end{itemize}

The data files are contained within one compressed
TAR file. Within that, they are as used in the original {\em Golem\/}
experiments. That is, background knowledge files have a ``.b'' suffix,
positive example files have a ``.f'' suffix, and negative example files
have a ``.n'' suffix.

\begin{thebibliography}{}

\bibitem{mugfeng:golem}
Muggleton S.H. and Feng C. (1990).
Efficient induction of logic programs.
{\sl Proceedings of the First Conference on Algorithmic Learning Theory},
Tokyo.

\bibitem{mugking:proteins}
Muggleton S., King R.D., and Sternberg M.J.E. (1992).
Predicting protein secondary structure using inductive logic programming.
{\sl Protein Engineering}, 5:647--657.

\end{thebibliography}

\end{document}
