The pore size and framework flexibility of hosts are of vital importance formolecular recognition and related applications, but accurate control of these parameters is very challenging. We use the slight difference of metal ion size to achieve continuous hundredth-nanometer pore-size adjustments and drastic flexibility modulations in an ultramicroporous metal–organic framework, giving controlla...

Background: Protein structures provide a valuable resource for rational drug design. For a protein with no known ligand, computational tools can predict surface pockets that are of suitable size and shape to accommodate a complementary small-molecule drug. However, pocket prediction against single static structures may miss features of pockets that arise from proteins’ dynamic behaviour. In par...

background and aim. the use of certain lasers has been proposed as an adjunctive method in periodontal pocket therapies. the objective of this study was to investigate the effects of nd:yag laser on the clinical periodontal parameters following scaling and root planing (srp) in comparison to spr alone. materials and methods. six adults with moderate to severe chronic periodontitis, each with at...

Sclareol is a high-value natural product obtained by solid/liquid extraction of clary sage (Salvia sclarea L.) inflorescences. Because processes of excretion and accumulation of this labdane diterpene are unknown, the aim of this work was to gain knowledge on its sites of accumulation in planta. Samples were collected in natura or during different steps of the industrial process of extraction (...

OBJECTIVE To assess the prevalence of gingival bleeding, calculus and periodontal pockets among 18-year-old males. In addition, to verify whether these conditions are associated with years of education and family income. METHODS A cross sectional survey was carried out. A representative sample of 18-year-old males living in Florianópolis, Brazil, was selected from the Brazilian Army applicant...

One of the simplest ways to predict ligand binding sites is to identify pocket-shaped regions on the protein surface. Many programs have already been proposed to identify these pocket regions. Examination of their algorithms revealed that a pocket intrinsically has two arbitrary properties, "size" and "depth". We proposed a new definition for pockets using two explicit adjustable parameters tha...

We have developed a new computational algorithm for de novo identification of protein-ligand binding pockets and performed a large-scale validation of the algorithm on two systematically collected datasets from all crystallographic structures in the Protein Data Bank (PDB). This algorithm, called DrugSite, takes a three-dimensional protein structure as input and returns the location, volume and...

Predicting protein pocket's ability to bind drug-like molecules with high affinity, i.e. druggability, is of major interest in the target identification phase of drug discovery. Therefore, pocket druggability investigations represent a key step of compound clinical progression projects. Currently computational druggability prediction models are attached to one unique pocket estimation method de...

The shape of a protein is important for its functions. This includes the location and size of identifiable regions in its complement space. We formally define pockets as regions in the complement with limited accessibility from the outside. Pockets can be efficiently constructed by an algorithm based on alpha complexes. The algorithm is implemented and applied to proteins with known three-dimen...