Emerging evidence indicates that membrane lipids regulate protein networking by directly interacting with protein-interaction domains (PIDs). As a pilot study to identify and functionally annodate lipid-binding PIDs on a genomic scale, we performed experimental and computational studies of PDZ domains. Characterization of 70 PDZ domains showed that ~40% had submicromolar membrane affinity. Usin...

Predicting protein secondary structure is a key step in determining the 3D structure of a protein that determines its function. The Dictionary of Secondary Structure of Proteins (DSSP) uses eight classes to describe a protein. The DSSP database is a database of secondary structure assignments for all protein entries in the Protein Data Bank (PDB) with an algorithm designed to standardize these ...

We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chain...

Protein microarrays, an emerging class of proteomic technologies, are fast becoming critical tools in biochemistry and molecular biology. Two classes of protein microarrays are currently available: analytical and functional protein microarrays. Analytical protein microarrays, mostly antibody microarrays, have become one of the most powerful multiplexed detection technologies. Functional protein...

At present, the feature extraction of protein sequences is the most basic issue to predict protein structural classes and is also the key problem to decide the quality of prediction. In order to predict protein structural classes accurately, we construct a 14-dimensional feature vector based on protein secondary and super-secondary structure information to reflect the content and spatial orderi...

Targeting the protein-protein interaction (PPI) between nuclear factor erythroid 2-related 2 (Nrf2) and Kelch-like ECH-associated protein 1 (Keap1) is a potential therapeutic strategy to control diseases involving oxidative stress. Here, six classes of known small-molecule Keap1-Nrf2 PPI inhibitors were dissected into 77 fragments in fragment-based deconstruction reconstruction (FBDR) study tes...