Abstract
We propose new empirical scoring potentials and associated alignment procedures for optimally aligning protein sequences to protein structures. The method has two main applications: first, the recognition of a plausible fold for a protein sequence of unknown structure out of a database of representative protein structures and, second, the improvement of sequence alignments by using structural information in order to find a better starting point for homology based modelling. The empirical scoring function is derived from an analysis of a nonredundant database of known structures by converting relative frequencies into pseudoenergies using a normalization according to the inverse Bolzmann law. These-so called contact capacity-potentials turn out to be discriminative enough to detect structural folds in the absence of significant sequence similarity and at the same time simple enough to allow for a very fast optimization in an alignment procedure.
Original language | English |
---|---|
Pages (from-to) | 53-72 |
Number of pages | 20 |
Journal | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing |
State | Published - 1996 |
Externally published | Yes |