Bioinformatics Vol. 17 no. 6 2001
Pages 541-550
© 2001 Oxford University Press
SCORE: predicting the core of protein models
1 Department of Biochemistry, University of
Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
2 ENSCM, 8 Rue de
L’école Normale, 34000,
Montpellier, France
Received on November 1, 2000
; revised on February 19, 2001
; accepted on February 23, 2001
Motivation: The prediction of the regions of homology models that can be ‘restrained by’ or ‘copied from’ the basis structures is a vital step in correct model generation, because these regions are the models most accurate part. However, there is no ideal method for the identification of their limits. In most algorithms their length depends on the number of family members and definitions of secondary structure.
Results: The algorithm SCORE steps away from the conventional
definitions of the core to identify from large numbers of basis
structures those regions that can be considered structurally related
to a target sequence. The use of 
constraints to
accurately pinpoint the regions that are conserved across a family
and environmentally constrained substitution tables to extend these
regions allows SCORE to rapidly (generally in under 1 s, an order of
magnitude faster than methods such as MODELLER) identify and build
the core of homology models from the alignments of the target
sequence to the basis structures. The SCORE algorithm was used to
build 114 model cores. In only two cases was the core size less than
50% of the structure and all the cores built had an RMSD of 3.7
Âor less to the target structure.
Availability: The algorithm is available upon request.
Contact: charlotte{at}cryst.bioc.cam.ac.uk
* To whom correspondence should be addressed.
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