Drug-target interaction prediction is an important problem for the development of novel drugs and human medical improvement. Many supervised and semi-supervised methods are proposed to uncover the relation between drugs and targets. Under the hypothesis that similar drugs target similar target proteins and the framework of Random Walk with Restart, the method of Networkbased Random Walk with Re...

Background: Endometriosis (EMT) is the most common benign gynecological disease among women of reproductive age, causing infertility and seriously affects women’s physical mental health. However, current treatment was not always effective. This study designed to use publicly available data identify drugs targeting relevant gene with EMT-induced-infertility using computational tools. Methods: EM...

Identifying the contact regions between a protein and its binding partners is essential for creating therapies that block the interaction. Unfortunately, such contact regions are extremely difficult to characterize because they are hidden inside the binding interface. Here we introduce protein painting as a new tool that employs small molecules as molecular paints to tightly coat the surface of...

Protein-protein interactions form the basis of many cellular processes. Disruption or deregulation of these complex interactions is the main cause of a significant number of human ailments. Consequently, there is intense research effort to design inhibitors that target specific protein-protein interactions. This places intricate protein-protein interactions in the heart of the development for n...

Most genes, proteins and other components carry out their functions within a complex network of interactions and a single molecule can affect a wide range of other cell components. A global, integrative, approach has been developed for several years, including protein-protein interaction networks (interactomes). In this review, we describe the high-throughput methods used to identify new intera...

The development of computational methods to discover novel drug-target interactions on a large scale is of great interest. We propose a new method for virtual screening based on protein interaction profile similarity to discover new targets for molecules, including existing drugs. We calculated Target Interaction Profile Fingerprints (TIPFs) based on ChEMBL database to evaluate drug similarity ...

We describe a graphical system for automatically generating multiple 2D diagrams of ligand-protein interactions from 3D coordinates. The diagrams portray the hydrogen-bond interaction patterns and hydrophobic contacts between the ligand(s) and the main-chain or side-chain elements of the protein. The system is able to plot, in the same orientation, related sets of ligand-protein interactions. T...

Employment of the decision strategies outlined in this general discussion should help to pinpoint mode of activity in drug development and validation. Overall, as a paradigm for drug development, a search for small molecules that can interfere with PPIs would seem to have significant long term potential. At present, the level of structural knowledge in databases is not sufficient to predict in ...