The structurally constrained protein evolution model accounts for sequence patterns of the LbetaH superfamily.

ABSTRACT:

Background

Structure conservation constrains evolutionary sequence divergence, resulting in observable sequence patterns. Most current models of protein evolution do not take structure into account explicitly, being unsuitable for investigating the effects of structure conservation on sequence divergence. To this end, we recently developed the Structurally Constrained Protein Evolution (SCPE) model. The model starts with the coding sequence of a protein with known three-dimensional structure. At each evolutionary time-step of an SCPE simulation, a trial sequence is generated by introducing a random point mutation in the current coding DNA sequence. Then, a "score" for the trial sequence is calculated and the mutation is accepted only if its score is under a given cutoff, lambda. Th

SUBMITTER: Parisi G 

PROVIDER: S-EPMC538250 | biostudies-literature | 2004 Oct

REPOSITORIES: biostudies-literature