MOTIVATION Interfacial water, which plays an important role in mediating biomolecular interactions, has been neglected in the modelling of biomolecular complexes. METHODS We present a solvated docking approach that explicitly accounts for the presence of water in protein-protein complexes. Our solvated docking protocol is based on the concept of the first encounter complex in which a water la...

Most state-of-the-art protein-protein docking algorithms use the Fast Fourier Transform (FFT) technique to sample the six-dimensional translational and rotational space. Scoring functions including shape complementarity, electrostatics, and desolvation are usually exploited in ranking the docking conformations. While these rigid-body docking methods provide good performance in bound docking, us...

Docking to the plasma membrane prepares vesicles for rapid release. Here, we describe a mechanism for dense core vesicle docking in neurons. In Caenorhabditis elegans motor neurons, dense core vesicles dock at the plasma membrane but are excluded from active zones at synapses. We have found that the calcium-activated protein for secretion (CAPS) protein is required for dense core vesicle dockin...

introduction:  stereotactic  radiosurgery  is  a  technique  for  the  treatment  of  intracranial  lesions  with  highly  collimated  x-ray  beam.  linac-based  radiosurgery  is  currently  performed  by  two  techniques:  couch or pedestal mounted. in the first technique, a device is required to affix patient's head to a couch  and  moreover  to  translate  it  accurately.  structure  of...

effects of partial docking on feedlot performance and body fat characteristics were studied in a fat-tailed sheep breed. thirty-eight male lambs with an average weight of 4.44 ± 0.48 were randomly divided into two groups. the lambs in one group were partially docked at 3-4 h after birth, using rubber rings, and the lambs in another group remained intact (control). after weaning, 20 male lambs f...

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...

modeling and simulation techniques are now widely used alongside with their experimental counterparts in order to complement them, or sometimes to bring first insights into the possible outcome of experiments. “modeling” is a general word that could encompass a wide range of methods that could be applied to a variety of subjects and problems. here, the use of selected molecular modeling methods...

Tail docking of pigs is a routine procedure on farms to help control tail-biting behavior; however, docking can cause pain. The objective of this research was to evaluate the effect of local or general anesthesia on the physiology (experiment 1) and behavior (experiment 2) of tail docked pigs. Pigs were allocated to one of six treatment groups: (i) sham docking (CON); (ii) docking using convent...

Dichloroacetate (DCA) is a simple and small anticancer drug that arouses the activity of the enzyme pyruvate dehydrogenase (PDH) through inhibition of the enzyme pyruvate dehydrogenase kinases (PDK1-4). DCA can selectively promote mitochondria-regulated apoptosis, depolarizing the hyperpolarized inner mitochondrial membrane potential to normal levels, inhibit tumor growth and reduce proliferati...

Dichloroacetate (DCA) is a simple and small anticancer drug that arouses the activity of the enzyme pyruvate dehydrogenase (PDH) through inhibition of the enzyme pyruvate dehydrogenase kinases (PDK1-4). DCA can selectively promote mitochondria-regulated apoptosis, depolarizing the hyperpolarized inner mitochondrial membrane potential to normal levels, inhibit tumor growth and reduce proliferati...