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...

BACKGROUND The rapid increase in antibiotic resistance by various bacterial pathogens underlies the significance of developing new therapies and exploring different drug targets. A fraction of bacterial pathogens abbreviated as ESKAPE by the European Center for Disease Prevention and Control have been considered a major threat due to the rise in nosocomial infections. Here, we compared putative...

Decisions on litigation spending can be viewed as constituting an iterated nonzero sum game, and thus as conducive to cooperation aimed at reducing spending. At the same time, though, litigants may engage in aggressive spending for various reasons, including a belief that they can outsmart the other party. This article uses a litigation simulation to consider how litigation spending is affected...

Identifying conserved pockets on the surfaces of a family of proteins can provide insight into conserved geometric features and sites of protein-protein interaction. Here we describe mapping and comparison of the surfaces of aligned crystallographic structures, using the protein kinase family as a model. Pockets are rapidly computed using two computer programs, FADE and Crevasse. FADE uses grad...

One of the factors limiting the search of new compounds based on the structure of target proteins involved in diseases is the limited amount of target structural information. Great advances in the search for lead compounds could be achieved to find new cavities in protein structures that are generated using well established computational chemistry tools. In the case of dengue, the discovery of ...

In this paper, we use the rotation number approach to study in detail the characteristic values of Hill’s equations with two-step periodic potentials. As a result, the global structure of resonance pockets is described completely. The results in this paper show that resonance pockets behave in a sensible and fairly rich way even in this simplest case.

conclusions the results of the present study suggest that the presence of fusobacterium species in periodontal pockets is an important risk factor for halitosis. results in total, 26% (n = 13) and 8% (n = 4) samples were positive for fusobacterium species in the halitosis and control groups, respectively, with f. nucleatum present in the greatest proportion in both groups. halitophobia was sign...

BACKGROUND Presentation of citrullinated neo-epitopes by HLA-DRB1 molecules that carry the shared epitope (SE) sequence was proposed to explain the association between HLA and seropositive RA. Although it is shown that several HLA-DRB1-SE molecules display enhanced binding affinities for citrullinated ligands, the ability of other HLA molecules to present citrullinated epitopes has not been inv...

The in-silico design of ligands binding to the protein surface instead of deep binding pockets is still a great challenge. Often no appropriate binding pockets are available in the apo experimental structures and standard virtual screening techniques will fail. Here, we present two new algorithms for designing tailored ligand binding pockets on the protein surface that account for protein backb...