A sequence family database built on ECOD structural domains.

ABSTRACT:

Motivation

The ECOD database classifies protein domains based on their evolutionary relationships, considering both remote and close homology. The family group in ECOD provides classification of domains that are closely related to each other based on sequence similarity. Due to different perspectives on domain definition, direct application of existing sequence domain databases, such as Pfam, to ECOD struggles with several shortcomings.

Results

We created multiple sequence alignments and profiles from ECOD domains with the help of structural information in alignment building and boundary delineation. We validated the alignment quality by scoring structure superposition to demonstrate that they are comparable to curated seed alignments in Pfam. Comparison to Pfam and CDD reve

SUBMITTER: Liao Y 

PROVIDER: S-EPMC6129306 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature