Motivation Large-scale computational docking will be increasingly used in future years to discriminate protein-protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein-protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations. ...

disposition and transportation of anticancer drugs by human serum albumin (hsa) affects their bioavailability, distribution and elimination. in this study, the interaction of a set of anticancer drugs with hsa was investigated by molecular dynamics and molecular docking simulations. the drugs' activities were analyzed according to their docking scores, binding sites and structural descriptors. ...

Due to the importance of longest path analysis in networks of queues, we develop an analytical method for computing the steady-state distribution function of longest path in acyclic networks of queues. We assume the network consists of a number of queuing systems and each one has either one or infinite servers. The distribution function of service time is assumed to be exponential or Erlang. Fu...

In practical situations, distribution network loads are the mixtures of residential, industrial, and commercial types. This paper presents a hybrid optimization algorithm for the optimal placement of shunt capacitor banks in radial distribution networks in the presence of different voltage-dependent load models. The algorithm is based on the combination of Genetic Algorithm (GA) and Binary Part...

The docking of synaptic vesicles at active zones on the presynaptic plasma membrane of axon terminals is essential for their fusion with the membrane and exocytosis of their neurotransmitter to mediate synaptic impulse transmission. Dense networks of macromolecules, called active zone material, (AZM) are attached to the presynaptic membrane next to docked vesicles. Electron tomography has shown...

Docking calculations have been conducted on 36 cellulase enzymes and the results were evaluated by a machine learning algorithm to determine the nature of the enzyme (i.e. endoor exoenzymatic activity). The docking calculations have also been used to identify crucial substrate-enzyme interactions, and establish structure-function relationships. The use of carboxymethyl cellulose as a docking su...

Core elements of cell regulation are made up of protein-protein interaction (PPI) networks. However, many parts of the cell regulatory systems include unknown PPIs. To approach this problem, we have developed a computational method of high-throughput PPI network prediction based on all-to-all rigid-body docking of protein tertiary structures. The prediction system accepts a set of data comprisi...

Optimization and reduction of costs in management of distribution and transportation of commodity are one of the main goals of many organizations. Using suitable models in supply chain in order to increase efficiency and appropriate location for support centers in logistical networks is highly important for planners and managers. Graph modeling can be used to analyze these problems and many oth...

In this study, a cross-docking system is designed at strategic and tactical levels. For making the strategic decisions, a multi-objective nonlinear location allocation model for cross-docks is presented based on a distri-bution location allocation model by Andreas Klose and Andreas Drexl. The model is further developed to in-clude the whole supply chain members and the objective functions are w...