Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed struct...

With advancements in crystallographic technology and the increasing wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information that will support the characterization of proteins and protein-ligand interactions. Herein, a new web service is presented termed amino acid frequency around ligand (AFAL) for determining amino ac...

Objective: Phenolic compounds have been considered inhibitors of various cancers. Material and Methods: In this study, caffeic acid and gallic acid were appraised for their possible effects on apoptotic genes expression in a breast cancer cell line in vitro. We also evaluated ligand interaction and ligand binding with estrogen receptor alpha by m...

Since its pandemic in 2019, SARS-CoV-2 has badly affected the countries around globe. There is no FDA approved drug for treatment of disease. In this study, we evaluated potential targets against non-structural protein-1 (Nsp-1), which crucial disturbing host-translational machinery. As completecrystal structure Nsp-1 was not available, used I-TASSER making complete protein. The verified using ...

BioLiP (http://zhanglab.ccmb.med.umich.edu/BioLiP/) is a semi-manually curated database for biologically relevant ligand-protein interactions. Establishing interactions between protein and biologically relevant ligands is an important step toward understanding the protein functions. Most ligand-binding sites prediction methods use the protein structures from the Protein Data Bank (PDB) as templ...

An abundance of protein structures emerging from structural genomics and the Protein Structure Initiative (PSI) are not amenable to ready functional assignment because of a lack of sequence and structural homology to proteins of known function. We describe a high-throughput NMR methodology (FAST-NMR) to annotate the biological function of novel proteins through the structural and sequence analy...

We use monodisperse dendrons that allow control over functional group presentation to investigate the influence of the location of a ligand on protein-induced disassembly and release of encapsulated small molecules. Based on both experiments and molecular dynamics simulations, we demonstrate that ligand location greatly influences release of guest molecules from the dendron-based supramolecular...

Morusin, an active constituent of the mulberry plant (Morus alba), exhibits inhibitory effects on several types cancer cells in vitro, including breast cancer. This study aimed to identify potential target proteins morusin, investigate binding energy, and explore type interactions between morusin protein. Morusin was searched using PubMed, STITCH, STRING, Cytoscape databases. Subsequently, obta...

Protein-protein interactions are challenging targets for modulation by small molecules. Here, we propose an approach that harnesses the increasing structural coverage of protein complexes to identify small molecules that may target protein interactions. Specifically, we identify ligand and protein binding sites that overlap upon alignment of homologous proteins. Of the 2,619 protein structure f...