Extended Abstract) 1 Motivation Protein structure prediction plays an important role in the fields of bioinformatics and biology. Traditional protein structure prediction approaches include template-based modeling (TBM, including homology modeling, and threading), and free modeling (FM). In particular, a threading algorithm takes a query protein sequence as input, recognizes the most likely fol...

Major goal of structural biology involve formation of protein-ligand complexes; in which the protein molecules act energetically in the course of binding. Therefore, perceptive of protein-ligand interaction will be very important for structure based drug design. Lack of knowledge of 3D structures has hindered efforts to understand the binding specificities of ligands with protein. With increasi...

Development of a phallus occurs in almost all amniotes; however, considerable variation in phallus morphology among different amniote lineages has contributed to the debate about their structural homology. Mammals are the only amniotes that form a closed urethral tube within the penis. In contrast, the phallus of reptiles and birds has an open urethral groove, or sulcus spermaticus, that facili...

Advances in protein crystallography and homology modeling techniques are producing vast amounts of high resolution protein structure data at ever increasing rates. As such, the ability to quickly and easily extract structural similarities is a key tool in discovering important functional relationships. We report on an approach for creating and maintaining a database of pairwise structure alignm...

The biological properties of proteins are often gleaned through comparative analysis of evolutionary relatives. Although protein structure similarity search methods detect more distant homologs than purely sequence-based methods, structural resemblance can result from either homology (common ancestry) or analogy (similarity without common ancestry). While many existing web servers detect struct...

Alpha-actinin is the major F-actin crosslinking protein in both muscle and non-muscle cells. We report the crystal structure of the actin binding domain of human muscle alpha-actinin-3, which is formed by two consecutive calponin homology domains arranged in a "closed" conformation. Structural studies and available biochemical data on actin binding domains suggest that two calponin homology dom...

Bacillus subtilis YdhG lacks sequence homology, but demonstrates structural and functional similarity to the frataxin family, supporting a general cellular role for frataxin-type proteins in cellular iron homeostasis.

The mammalian poly(ADP-ribose) polymerase (PARP) family includes ADP-ribosyltransferases with diphtheria toxin homology (ARTD). Most members have mono-ADP-ribosyltransferase activity. PARP13/ARTD13, also called zinc finger antiviral protein, has roles in viral immunity and microRNA-mediated stress responses. PARP13 features a divergent PARP homology domain missing a PARP consensus sequence moti...

A novel protein, PID-5, has been shown to be a requirement for germline immortality and recently implicated in RNA-induced epigenetic silencing the Caenorhabditis elegans embryo. Importantly, it contain both an eTudor aminopeptidase P-related domain. However, mechanism not yet fully characterised. In this study, bioinformatic tools were used compare pre-existing P molecular structures AlphaFold...

BACKGROUND Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and ...