Gap junctions are unique intercellular channels formed by the proper docking of two hemichannels from adjacent cells. Each hemichannel is a hexamer of connexins (Cxs) - the gap junction subunits, which are encoded by 21 homologous genes in the human genome. The docking of two hemichannels to form a functional gap junction channel is only possible between compatible Cxs, but the underlying molec...

MOTIVATION Protein-protein interactions are a key in virtually all biological processes. For a detailed understanding of the biological processes, the structure of the protein complex is essential. Given the current experimental techniques for structure determination, the vast majority of all protein complexes will never be solved by experimental techniques. In lack of experimental data, comput...

In this work we develop a method for fluid dynamically driven assembly in three dimensions and demonstrate its applicability to the development of programmable matter. Towards this end, we investigate docking of a single block onto a larger structure using detailed numerical simulations and experiments. Our simulation results show that a block whose degrees of freedom are limited is able to ali...

The reversible process between distributed robots and connected robot is the key issue of mobile self-reconfigurable robots, which can be divided into two phases of aggregation and docking. In this paper, corresponding strategies are proposed for robots enhanced with mobility. In the dynamic aggregation mechanisms, the optimal locations are determined based on the multi-object optimization of t...

The protein-protein docking server ClusPro is used by thousands of laboratories, and models built by the server have been reported in over 300 publications. Although the structures generated by the docking include near-native ones for many proteins, selecting the best model is difficult due to the uncertainty in scoring. Small angle X-ray scattering (SAXS) is an experimental technique for obtai...

Inhibition of the Tryparedoxin peroxidase interaction has been becomes a new therapeutic strategy in leishmaniasis. Docking analysis was carried out to study the effects of quercetin and taxifolin on Tryparedoxin Peroxidase (TryP). Tryparedoxin peroxidase of Trypanosomatidae functions as antioxidants through their Peroxidase and peroxynitrite reductase activities. The 3D models of Tryparedoxin ...

Neisseria meningitidis elicits the formation of membrane protrusions on vascular endothelial cells, enabling its internalization and transcytosis. We provide evidence that this process interferes with the transendothelial migration of leukocytes. Bacteria adhering to endothelial cells actively recruit ezrin, moesin, and ezrin binding adhesion molecules. These molecules no longer accumulate at s...

DNA methylation is a covalent chemical modification of DNA catalyzed by DNA methyltransferases (DNMTs) and plays a crucial role in epigenetic modifications. Inhibition of DNMT is a promising strategy for the treatment of various developmental and proliferative diseases, particularly cancers. Molecular docking and other computational approaches are increasingly being used to explore the ligand-b...

The Surflex flexible molecular docking method has been generalized and extended in two primary areas related to the search component of docking. First, incorporation of a small-molecule force-field extends the search into Cartesian coordinates constrained by internal ligand energetics. Whereas previous versions searched only the alignment and acyclic torsional space of the ligand, the new appro...

in the recent years, targeted therapy of the neoplastic diseases is a current strategy used by oncologists. hence, design and discovery of novel targeted anticancer therapeutics is an interesting topic in the current research of medicinal chemistry. a new series of 1,3,4-thiadiazole derivatives were prepared and their anticancer activity was assessed against pc3, sknmc and ht29 cell lines by ap...