A comprehensive manually curated protein–protein interaction database for the Death Domain superfamily

Abstract

The Death Domain (DD) superfamily, which is one of the largest classes of protein interaction modules, plays a pivotal role in apoptosis, inflammation, necrosis and immune cell signaling pathways. Because aberrant or inappropriate DD superfamily-mediated signaling events are associated with various human diseases, such as cancers, neurodegenerative diseases and immunological disorders, the studies in these fields are of great biological and clinical importance. To facilitate the understanding of the molecular mechanisms by which the DD superfamily is associated with biological and disease processes, we have developed the DD database (http://www.deathdomain.org), a manually curated database that aims to offer comprehensive information on protein–protein interactions (PPIs) of the DD superfamily. The DD database was created by manually curating 295 peer-reviewed studies that were published in the literature; the current version documents 175 PPI pairs among the 99 DD superfamily proteins. The DD database provides a detailed summary of the DD superfamily proteins and their PPI data. Users can find in-depth information that is specified in the literature on relevant analytical methods, experimental resources and domain structures. Our database provides a definitive and valuable tool that assists researchers in understanding the signaling network that is mediated by the DD superfamily.

Fuzzy support vector machine model to predict human death domain protein–protein interactions

“…Since no model is reported in the literature for prediction of human death domain protein-protein interaction via fuzzy support vector machine approach and therefore, no existing theoretical results are available for comparison. However, the results obtained in this study are in agreement with the available experimental data of proteinprotein interaction of death domain proteins (Kwon et al 2012).…”

“…The data of human death domain protein-protein interaction are collected from the death domain database (Kwon et al 2012). The redundancy in the data set is identified and removed to obtain non-redundant data set.…”

“…Therefore, the data are collected from death domain (DD) database (Kwon et al 2012) which is maintained at www. deathdomain.org website, including two known class death related (positive data set) and death unrelated (negative data set) which makes it two class prediction problem.…”

Structure of the Absent in Melanoma 2 (AIM2) Pyrin Domain Provides Insights into the Mechanisms of AIM2 Autoinhibition and Inflammasome Assembly

“…AIM2 was also reported to play a role in autoimmune disorders such as psoriasis through recognition of host DNA (10). It belongs to the pyrin and HIN protein (PYHIN) family of proteins that includes interferon ␥-inducible protein 16 (11), IFN-inducible protein X/PYHIN1, and myeloid cell nuclear differentiation antigen in the human genome (12,13). AIM2 contains a carboxyl-terminal HIN domain that binds dsDNA and an amino-terminal PYD that is responsible for downstream signaling to the adapter protein ASC.…”

“…PYDs-There are a total of 22 PYD-containing proteins in the human genome (13), including the PYHIN proteins, the NLR family members NLRP1-14, the pyrin protein encoded by the Mediterranean fever gene, the adapter protein ASC, and PYD-only proteins (POPs) POP1/ASC2 and POP2. A sequence alignment of these PYDs guided by the known structures reveals that several conserved residues are shared between the PYHIN PYDs and other PYDs (Fig.…”