Current opinion in structural biology
Dec 23, 2021
Proteins interact through their interfaces to fulfill essential functions in the cell. They bind to their partners in a highly specific manner and form complexes that have a profound effect on understanding the biological pathways they are involved i...
Biochemical and biophysical research communications
Dec 20, 2021
Apoptosis plays an essential role in maintaining cellular homeostasis and preventing cancer progression. Bcl-xL, an anti-apoptotic protein, is an important modulator of the mitochondrial apoptosis pathway and is a promising target for anticancer ther...
One important aspect of protein function is the binding of proteins to ligands, including small molecules, metal ions, and macromolecules such as DNA or RNA. Despite decades of experimental progress many binding sites remain obscure. Here, we propose...
Accurate quantification of protein-ligand interactions remains a key challenge to structure-based drug design. However, traditional machine learning (ML)-based methods based on handcrafted descriptors, one-dimensional protein sequences, and/or two-di...
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Dec 4, 2021
Ranging from bacterial cell adhesion over viral cell entry to human innate immunity, glycan-binding proteins or lectins are abound in nature. Widely used as staining and characterization reagents in cell biology and crucial for understanding the inte...
In this paper, we propose a simple descriptor called the ligand coordinate profile (LCP) for describing docking poses. The LCP descriptor is generated from the coordinates of the polar hydrogen and heavy atoms of the docked ligand. We hypothesize tha...
Resistance to small-molecule drugs is the main cause of the failure of therapeutic drugs in clinical practice. Missense mutations altering the binding of ligands to proteins are one of the critical mechanisms that result in genetic disease and drug r...
Journal of chemical theory and computation
Nov 18, 2021
An unsolved challenge in the development of antigen-specific immunotherapies is determining the optimal antigens to target. Comprehension of antigen-major histocompatibility complex (MHC) binding is paramount toward achieving this goal. Here, we appl...
The biological significance of proteins attracted the scientific community in exploring their characteristics. The studies shed light on the interaction patterns and functions of proteins in a living body. Due to their practical difficulties, reliabl...
The journal of physical chemistry letters
Nov 9, 2021
No anti-cocaine addiction drugs have been approved by the Food and Drug Administration despite decades of effort. The main challenge is the intricate molecular mechanisms of cocaine addiction, involving synergistic interactions among proteins upstrea...