Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures.

ABSTRACT: Structural classifications of proteins assume the existence of the fold, which is an intrinsic equivalence class of protein domains. Here, we test in which conditions such an equivalence class is compatible with objective similarity measures. We base our analysis on the transitive property of the equivalence relationship, requiring that similarity of A with B and B with C implies that A and C are also similar. Divergent gene evolution leads us to expect that the transitive property should approximately hold. However, if protein domains are a combination of recurrent short polypeptide fragments, as proposed by several authors, then similarity of partial fragments may violate the transitive property, favouring the continuous view of the protein structure space. We propose a measure to quanti

SUBMITTER: Pascual-Garcia A 

PROVIDER: S-EPMC2654728 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature