UNLABELLED Sliding Box Docking is a program that manages simulations of ligand docking at different defined positions of a three-dimensional DNA structure. The procedure is similar to inverse docking, which is a method that performs docking simulations of a single ligand in the active sites of different targets. Sliding Box Docking manages docking simulations of one ligand into a box that slide...

Vacuole inheritance in yeast involves the formation of tubular and vesicular "segregation structures" which migrate into the bud and fuse there to establish the daughter cell vacuole. Vacuole fusion has been reconstituted in vitro and may be used as a model for an NSF-dependent reaction of priming, docking, and fusion. We have developed biochemical and microscopic assays for the docking step of...

histone deacetylase inhibitors have gained a great deal of attention recently for the treatment of cancers and inflammatory diseases. so design of new inhibitors is of great importance in pharmaceutical industries and labs. creating pharmacophor models in order to design new molecules or search a library for finding lead compounds is of great interest. this approach reduces the overall cost ass...

A combination of protein-ligand docking and ligand-based QSAR approaches has been elaborated, aiming to speed-up the process of virtual screening. In particular, this approach utilizes docking scores generated for already processed compounds to build predictive QSAR models that, in turn, assess hypothetical target binding affinities for yet undocked entries. The "progressive docking" has been t...

Virtual screening by molecular docking has become a widely used approach to lead discovery in the pharmaceutical industry when a high-resolution structure of the biological target of interest is available. The performance of three widely used docking programs (Glide, GOLD, and DOCK) for virtual database screening is studied when they are applied to the same protein target and ligand set. Compar...

Docking, the initial association of secretory vesicles with the plasma membrane, precedes formation of the SNARE complex, which drives membrane fusion. For many years, the molecular identity of the docked state, and especially the vesicular docking protein, has been unknown, as has the link to SNARE complex assembly. Here, using adrenal chromaffin cells, we identify the vesicular docking partne...

A pharmaceutical drug compound is usually a small organic molecule, also termed as ligand, that binds to the target protein and alters the natural activity of the protein, thus, leading to a therapeutic effect. Computational docking or computer-aided docking is an extremely useful tool to gain an understanding of protein-ligand interactions which is important for the drug discovery. Computation...

It is well known that computer-aided docking of large ligands, with many rotatable bonds, is extremely difficult. AutoDock is a widely used docking program that can dock small ligands, with upto 5 or 6 rotatable bonds, accurately and quickly. Docking of larger ligands, however, is not very accurate and is computationally expensive. In this paper we present an AutoDock-based incremental docking ...

The Hardware-In-the-Loop (HIL) simulation system for on-orbit docking dynamics is a large-scale complex test equipment. It establishes working conditions for the docking mechanism similar with those on orbit. The kernel of above dynamics HIL simulation system is a mechanical force and movement actions simulator. Besides the mechanical force and movement actions simulator, it also includes an en...

Bike sharing systems consist of a fleet of bikes placed in a network of docking stations. These bikes can then be rented and returned to any of the docking stations after usage. Predicting unrealized bike demand at locations currently without bike stations is important for effectively designing and expanding bike sharing systems. We predict pairwise bike demand for New York City’s Citi Bike sys...