A. Ableson and J.I. Glasgow
Abstract
Crystallographic studies play
a major role in current efforts towards protein structure determination.
Despite recent advances in computational tools for molecular modeling
and graphics, the construction of a three-dimensional protein
backbone model from crystallographic data remains complex and
time-consuming. This paper describes a unique contribution to
an automated approach to protein model construction and evaluation,
where a model is represented as an annotated trace (or partial
trace) of a structure. Candidate models are derived through a
topological analysis of the electron density map of a protein.
Using sequence alignment techniques, we determine an optimal threading
of the known sequence onto the candidate protein structure models.
In this threading, connected nodes on the model are associated
with adjacent amino acids in the sequence and a fitness score
is assigned based on features extracted from the electron density
map for the protein. Experimental results demonstrate that crystallographic
threading provides an effective means for evaluating the "goodness"
of experimentally derived protein models.