Voids and pockets in a protein refer to empty spaces that are enclosed by the protein molecule. Existing methods to compute, measure, and visualize the voids and pockets in a protein molecule are sensitive to inaccuracies in the empirically determined atomic radii. This paper presents a topological framework that enables robust computation and visualization of these structures. Given a fixed se...

Moderate-to-severe chronic periodontitis results in clinical loss of attachment, reduced width of attached gingiva (AG), periodontal pockets beyond mucogingival junction (MGJ), gingival recession, loss of alveolar bone, and decreased vestibular depth (VD). The encroachment of frenal and muscle attachments on marginal gingiva increases the rate of progression of periodontal pockets, prevents hea...

Multiple beam interferometry and video microscopy were used to investigate the layering transition of thin liquid films of 1-undecanol confined between atomically smooth mica surfaces. The expulsion of a molecularly thin lubricant layer was followed directly in two dimensions. Overall, the dynamics of the transition follows theoretical predictions based on two-dimensional hydrodynamics. Frequen...

Motivation: Prediction of ligands for proteins of known 3D structure is important to understand structurefunction relationship, predict molecular function, or design new drugs. Results: We explore a new approach for ligand prediction in which binding pockets are represented by atom clouds. Each target pocket is compared to an ensemble of pockets of known ligands. Pockets are aligned in 3D space...

V.parahaemolyticus pathogenicity has been associated with its ability to produce thermostable direct hemolysin (TDH) encoded by the tdh gene. Although all V.parahaemolyticus strains possess this gene some strains are hemolytic, intermediate or non-hemolytic. To assess the differences seen, we screened the surface of the TDH proteins showing variable hemolytic activity for identification of poss...

The problem addressed is reconfiguration planning for a metamorphic robotic system composed of any number of hexagonal robots when multiple simple obstacles are embedded in the goal environment. Simple obstacles are defined as obstacles that have even surfaces with no pockets or indentations and that, as a group, form no narrow corridors or isolated areas. We extend our earlier work on filling ...

Modern research confirms the role of inflammatory mediators in the pathomechanism of periodontal tissue destruction. The aim of the study was to determine concentrations of MMP-8 and IL-1β in gingival crevicular fluid (GCF) in patients with advanced chronic and aggressive periodontitis. The authors measured the concentrations of the above inflammatory mediators in gingival crevicular fluid of d...

In this paper, we develop an autonomous construction system in which a self-contained ground robot builds a protective barrier by means of compliant pockets (i.e., filled bags). We present a stochastic control algorithm based on two biological mechanisms (stigmergy and templates) that takes advantage of compliant pockets for autonomous construction. The control algorithm guides the robot to bui...

g-secretase is responsible for the proteolysis of amyloid precursor protein (APP) into short, aggregation-prone amyloid-beta (Ab) peptides, which are centrally implicated in the pathogenesis of Alzheimer’s disease (AD). Despite considerable interest in developing g-secretase targeting therapeutics for the treatment of AD, the precise mechanism by which g-secretase produces Ab has remained elusi...

Because of the relevance of d-serine (d-Ser) to schizophrenia, inhibitors of d-amino acid oxidase (DAO), which catalyzes degradation of d-Ser in the presence of flavin adenine dinucleotide (FAD), are expected to be anti-schizophrenia therapeutics. In this study, binding pockets of DAO to its inhibitor 4-bromo-3-nitrobenzoic acid were searched by combining in silico docking simulation and labeli...