Shape space was proposed by Perelson and Oster 20 years ago as a conceptual formalism in which to represent antibody/antigen binding. It has since played a key role in computational immunology. Antigens and antibodies are thought of as points in an abstract "shape space" where coordinates of...

Recently, there has been considerable interest in deriving and applying knowledge-based, empirical potential functions for proteins. These empirical potentials have been derived from the statistics of interacting, spatially neighboring residues, as may be obtained from databases of known protein...

We present a method for calculating the ``noise sensitivity signature'' of a learning algorithm which is based on scrambling the output of classes of various fractions of the training data. This signature can be used to indicate a good (or bad) match between the complexity of the classifier and...

Our previous work applied neural network techniques to the problem of discriminating open reading frame (ORF) sequences taken from introns versus exons. The method counted the codon frequencies in an ORF of a specified length, and then used this codon frequency representation of DNA fragments to...

A comparison of neural network methods, and Bayesian statistical methods, is presented for prediction of the secondary structure of proteins given their primary sequence. The Bayesian method makes the unphysical assumption that the probability of an amino acid occurring in each position in the...

A criterion based on conditional probabilities, related to the concept of algorithmic distance, is used to detect correlated mutations at noncontiguous sites on sequences. We apply this criterion to the problem of analyzing correlations between sites in protein sequences, however, the analysis...

We show how randomly scrambling the output of classes of various fractions of the training data may be used to improve predictive accuracy of a classification algorithm. We present a method for calculating the ``noise sensitivity signature'' of a learning algorithm which is based on scrambling...