Conserved Domain Database (CDD): Bringing structural biology closer to the biologist

Tuesday, October 09, 2012 — Poster Session I
1:00 p.m. – 3:00 p.m	Natcher Conference Center, Building 45	NLM	BIOINFO-5

Authors

• M.K. Derbyshire
• S. Lu
• F. Chitsaz
• L.Y. Geer
• R.C. Geer
• N.R. Gonzales
• M. Gwadz
• D.I. Hurwitz
• C.J. Lanczycki
• F. Lu
• G.H. Marchler
• J.S. Song
• N. Thanki
• R.A. Yamashita
• D. Zhang
• C. Zheng
• S.H. Bryant
• A. Marchler-Bauer

Abstract

The Protein Structure Initiative (PSI) represents a significant investment in structural biology and has led to a wealth of 3D-data characterizing many protein domain families. Its initial approach of determining novel structures indiscriminately has been criticized for a lack of impact on biomedical research, though this surge in raw data may also require better tools for the bench-biologists, so that they can utilize 3D-data more productively. NCBI’s Structure Group provides access to data derived from 3D structure, by maintaining a mirror of PDB complete with structure neighboring and tracking of molecular interactions, by establishing an archive of small molecules and information on their interactions with biological systems, and by maintaining CDD, a protein and domain family classification system. CDD uses 3D-data to detect or verify remote homologous relationships, to build accurate domain family models and classifications, to infer molecular function for previously uncharacterized families, and to annotate functional sites. CDD maintains a high level of coverage of protein structures with domain annotation, by building new family models. We present statistics on domain families curated as part of this activity, and show how 3D-data guides the annotation of functional sites, which complement site annotations from other curated collections.

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