Synaptic vesicle docking, priming, and fusion at active zones are orchestrated by a complex molecular machinery. We employed hippocampal organotypic slice cultures from mice lacking key presynaptic proteins, cryofixation, and three-dimensional electron tomography to study the mechanism of synaptic vesicle docking in the same experimental setting, with high precision, and in a near-native state....

Molecular docking is routinely used for understanding drug-receptor interaction in modern drug design. Here, we describe the docking of 2, 4-diamino-5-methyl-5-deazapteridine (DMDP) derivatives as inhibitors to human dihydrofolate reductase (DHFR). We docked 78 DMDP derivates collected from literature to DHFR and studied their specific interactions with DHFR. A new shape-based method, LigandFit...

Secretory vesicles dock at their target in preparation for fusion. Using single-vesicle total internal reflection fluorescence microscopy in chromaffin cells, we show that most approaching vesicles dock only transiently, but that some are captured by at least two different tethering modes, weak and strong. Both vesicle delivery and tethering depend on Munc18-1, a known docking factor. By decrea...

Summary We present an approach for the efficient docking of peptide motifs to their free receptor structures. Using a motif based search, we can retrieve structural fragments from the Protein Data Bank (PDB) that are very similar to the peptide's final, bound conformation. We use a Fast Fourier Transform (FFT) based docking method to quickly perform global rigid body docking of these fragments ...

ATP is involved in numerous biochemical reactions in living cells interacting with different proteins. Molecular docking simulations provide considerable insight into the problem of molecular recognition of this substrate. To improve the selection of correct ATP poses among those generated by docking algorithms we propose a post-docking reranking criterion. The method is based on detailed analy...

This article reports on a reactive docking behavior which uses a vision algorithm that grows linearly with the number of image pixels. The docking robot imprints (initializes) on a twocolored docking ducial upon departing from the dock, then uses region statistics to adapt the color segmentation in changing lighting conditions. The docking behavior was implemented on a marsupial team of robots,...

Docking by knife or elastrator had no sustained effect on growth of lambs 0 to 8 wk postpartum. However, during the 2 wk period postdocking, growth of lambs was limited or depressed, regardless of whether lambs were docked by knife at 14, 28 or 42 d of age. Blood hematocrit and hemoglobin were decreased (P less than .01) 1 d after docking by knife and 14 d after docking by elastrator. Neither m...

Microelectromechanical system (MEMS) technology promises to improve performance of future spacecraft components while reducing mass, cost, and manufacturing time. Arrays of microcilia actuators offer a lightweight alternative to conventional docking systems for miniature satellites. Instead of mechanical guiding structures, such a system uses a surface tiled with MEMS cilia actuators to guide t...

The main key to success in structure-based drug discovery is the accurate prediction of binding affinities of hit compounds. Molecular docking and scoring functions are often used for this purpose. However, it is often found that the top-ranked docking poses do not represent the right binding mode, and frequently there is no correlation between docking score and biological data. Therefore, “pos...

Structural details of protein-protein interactions are invaluable for understanding and deciphering biological mechanisms. Computational docking methods aim to predict the structure of a protein-protein complex given the structures of its single components. Protein flexibility and the absence of robust scoring functions pose a great challenge in the docking field. Due to these difficulties most...