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

Cellular functions require specific protein-protein interactions that are often mediated by modular domains that use binding pockets to engage particular sequence motifs in their partners. Yet, how different members of a domain family select for distinct sequence motifs is not fully understood. The human genome encodes 120 Src homology 2 (SH2) domains (in 110 proteins), which mediate protein-pr...

Protein–ligand binding is a key biological process at the molecular level. The identification and characterization of small-molecule binding sites on therapeutically relevant proteins have tremendous implications for target evaluation and rational drug design. In this work, we used the recently developed level-set variational implicit-solvent model (VISM) with the Coulomb field approximation (C...

RNA-binding proteins play a significant role in pattern regulation of gene expression during developmental phases. Therefore in order to facilitate our understanding of organism development there is a continuous need to develop an extensive a priori method for the prediction of RNA-binding protein pockets. We present here a SVM (Support Vector Machine) based approach for successful prediction o...

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...

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...