Neuronal exocytosis is mediated by the SNARE proteins synaptobrevin 2/VAMP, syntaxin 1A, and SNAP-25A. While it is well-established that these proteins mediate membrane fusion after reconstitution in artificial membranes, it has so far been difficult to monitor intermediate stages of the reaction. Using a confocal two-photon setup, we applied fluorescence cross-correlation spectroscopy (FCCS) a...

In this work, we propose a deep learning approach to improve docking-based virtual screening. The deep neural network that is introduced, DeepVS, uses the output of a docking program and learns how to extract relevant features from basic data such as atom and residues types obtained from protein-ligand complexes. Our approach introduces the use of atom and amino acid embeddings and implements a...

A novel contour-based matching criterion is presented for the quantitative docking of high-resolution structures of components into low-resolution maps of macromolecular complexes. The proposed Laplacian filter is combined with a six-dimensional search using fast Fourier transforms to rapidly scan the rigid-body degrees of freedom of a probe molecule relative to a fixed target density map. A co...

in the present study, the antimicrobial tests of patchouli oil were studied by using molecular docking technology and antimicrobial test in vitro. five biological macromolecule enzymes, required by the bacteria in the process of biosynthesis were selected as target molecules. five antibiotics benzylpenicillin, sulfadiazine, trimethoprim, rifampicin and ciprofloxacin, which are generally acknowle...

the antidiuretic effect of arginine vasopressin (avp) is mediated by the vasopressin v2 receptor. the docking study of avp as a ligand to v2 receptor helps in identifying important amino acid residues that might be involved in avp binding for predicting the lowest free energy state of the protein complex. whereas previous researchers were not able to detect the exact site of the ligand-receptor...

objective(s): recently we reported that the soybean 15-lipoxygenase (slo) inhibitory activity of pyrimido[4,5-b][l,4]benzothiazines largely depends on the orientation of sulfur atom of thiazine core towards feiii-oh in the active site pocket of the enzyme with subsequent oxidation of sulfur to sulfoxide. in this paper the results of a comparative study on the slo inhibitory activities of the me...

background: luxi is a component of the quorum sensing signaling pathway in vibrio fischeri responsible for the inducer synthesis that is essential for bioluminescence. methods: homology modeling of luxi was carried out using phyre2 and refined with the galaxyweb server. five models were generated and evaluated by errat, anolea, qmean6, and procheck. results: five refined models were generated b...