We present Fleksy, a new approach to consider both ligand and receptor flexibility in small molecule docking. Pivotal to our method is the use of a receptor ensemble to describe protein flexibility. To construct these ensembles, we use a backbone-dependent rotamer library and implement the concept of interaction sampling. The latter allows the evaluation of different orientations of ambivalent ...

In the context of Remotly Operated Vehicule (ROV) for underwater application, connecting the robot to its docking station can be a significant challenge [2]. ROV have to navigate in a complex and unpredictable environment since the perception is limitted. Optical and Acoustic sensor can not be used is this kind of environment because blind spots can occur and short range obstacles may interfere...

Locating distribution centers optimally is a crucial and systematic task for logistic operators and decision makers. Optimally located distribution centers can significantly improve the logistic system’s efficiency and reduce its operational cost. However, it is not an easy task to optimize distribution center locations and previous studies focused primarily on location optimization of a single...

Community corrections centers (CCCs) are known to be an effective criminal justice strategy. However, location of CCCs is challenging: residents of potential destination communities often regard them as “undesirable” land uses. We develop a methodology by which a small set of feasible CCC locations may be identified from a larger initial set using data on neighborhood characteristics and curren...

A crucial question in the design of ecient logistics systems is the identi®cation of locations for distribution centers (DCs). However, the optimization of these location decisions requires careful attention to the inherent trade-o€s among facility costs, inventory costs, transportation costs, and customer responsiveness. This paper presents a modeling approach that provides such an integrated...

BACKGROUND Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this re...

  We consider the maximal covering location-allocation problem with multiple servers. The objective is to maximize the population covered, subject to constraints on the number of service centers, total number of servers in all centers, and the average waiting time at each center. Each center operates as an M/M/k queuing system with variable number of servers. The total costs of establishing cen...

T cells are known to cross-react with diverse peptide MHC Ags through their alphabeta TCR. To explore the basis of such cross-reactivity, we examined the 2C TCR that recognizes two structurally distinct ligands, SIY-K(b) and alloantigen QL9-L(d). In this study we characterized the cross-reactivity of several high-affinity 2C TCR variants that contained mutations only in the CDR3alpha loop. Two ...

This study considers a combination of cross-docking and vehicle routing problem (VRP) approachesto transport raw material and parts in a supply chain. The supply chain is composed of some supplierswhich are spread in different geographical zones and multiple shared vehicles with different speedsand capacities for transporting orders from the suppliers to a manufacturer. After ...

One of the most important issues in area of health and hygiene is location-allocation of organ harvesting centers and transplant centers according to coordination between supply and demand. In this paper, a mathematical model is presented for location-allocation of organ harvesting centers and transplant centers. The proposed model does not only minimize the present value of the total system co...