IS-Dom: a dataset of independent structural domains automatically delineated from protein structures

• Published in: Journal of computer-aided molecular design Vol. 27; no. 5; pp. 419 - 426
• Main Authors: Ebina, Teppei, Umezawa, Yuki, Kuroda, Yutaka
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.05.2013; Springer Nature B.V
• Subjects: Algorithms; Animal Anatomy; Biotechnology; CAD; Chemistry; Chemistry and Materials Science; Computational Biology; Computer aided design; Computer Applications in Chemistry; Databases, Protein; Histology; Molecular chemistry; Morphology; Physical Chemistry; Protein Conformation; Protein Folding; Protein Structure, Tertiary; Proteins; Proteins - chemistry; Proteomics; Sequence Analysis, Protein; Software; Structural domains; High-throughput; DomainParser; SCOP; Proteomics; Domain prediction; Domain database; Protein dissection; Autonomously folded; CATH
• ISSN: 0920-654X; 1573-4951
• DOI: 10.1007/s10822-013-9654-6

Protein domains that can fold in isolation are significant targets in diverse area of proteomics research as they are often readily analyzed by high-throughput methods. Here, we report IS-Dom, a dataset of Independent Structural Domains (ISDs) that are most likely to fold in isolation. IS-Dom was constructed by filtering domains from SCOP, CATH, and DomainParser using quantitative structural measures, which were calculated by estimating inter-domain hydrophobic clusters and hydrogen bonds from the full length protein’s atomic coordinates. The ISD detection protocol is fully automated, and all of the computed interactions are stored in the server which enables rapid update of IS-Dom. We also prepared a standard IS-Dom using parameters optimized by maximizing the Youden’s index. The standard IS-Dom, contained 54,860 ISDs, of which 25.5 % had high sequence identity and termini overlap with a Protein Data Bank (PDB) cataloged sequence and are thus experimentally shown to fold in isolation [coined autonomously folded domain (AFDs)]. Furthermore, our ISD detection protocol missed less than 10 % of the AFDs, which corroborated our protocol’s ability to define structural domains that are able to fold independently. IS-Dom is available through the web server ( http://domserv.lab.tuat.ac.jp/IS-Dom.html ), and users can either, download the standard IS-Dom dataset, construct their own IS-Dom by interactively varying the parameters, or assess the structural independence of newly defined putative domains.