DiPPI: A Curated Data Set for Drug-like Molecules in Protein-Protein Interfaces.

Proteins interact through their interfaces, and dysfunction of protein-protein interactions (PPIs) has been associated with various diseases. Therefore, investigating the properties of the drug-modulated PPIs and interface-targeting drugs is critical. Here, we present a curated large data set for drug-like molecules in protein interfaces.

Conformational diversity and protein-protein interfaces in drug repurposing in Ras signaling pathway.

We focus on drug repurposing in the Ras signaling pathway, considering structural similarities of protein-protein interfaces. The interfaces formed by physically interacting proteins are found from PDB if available and via PRISM (PRotein Interaction by Structural Matching) otherwise. The structural coverage of these interactions has been increased from 21 to 92% using PRISM.

ASCARIS: Positional feature annotation and protein structure-based representation of single amino acid variations.

Background: Genomic variations may cause deleterious effects on protein functionality and perturb biological processes. Elucidating the effects of variations is critical for developing novel treatment strategies for diseases of genetic origin. Computational approaches have been aiding the work in this field by modeling and analyzing the mutational landscape.

Salubrinal Ameliorates Inflammation and Neovascularization via the Caspase 3/Enos Signaling in an Alkaline-Induced Rat Corneal Neovascularization Model.

Ocular alkaline burn is a clinical emergency that can cause permanent vision loss due to limbal stem cell deficiency and corneal neovascularization (CNV). Although the basic pathogenetic mechanisms are considered to be acute oxidative stress and corneal neovascularization triggered by inflammation, the underlying intracellular mechanisms have not been clearly elucidated. The aim of this study was to investigate the role of endoplasmic reticulum (ER) stress on inflammation and neovascularization, and the effect of the ER stress inhibitor salubrinal (SLB), as a novel treatment in a corneal alkaline burn model in rats.

Artificial intelligence approaches to human-microbiome protein-protein interactions.

Host-microbiome interactions play significant roles in human health and disease. Artificial intelligence approaches have been developed to better understand and predict the molecular interplay between the host and its microbiome. Here, we review recent advancements in computational methods to predict microbial effects on human cells with a special focus on protein-protein interactions.