In a supply chain, cross-docking is one of the most innovative systems for ameliorating the operational performance at distribution centers. Cross-docking is a logistics strategy in which freight is unloaded from inbound trucks and (almost) directly loaded into outbound trucks, with little or no storage in between, thus no inventory remains at the distribution center. In this study, we consider...

The vehicle routing problem with cross-docking (VRPCD) consists in defining a set of routes that satisfy transportation requests between a set of pickup points and a set of delivery points. The vehicles bring goods from pickup locations to a cross-docking platform, where the items may be consolidated for efficient delivery. In this paper we propose a new solution methodology for this problem. I...

BACKGROUND Safer and more effective mixtures of anticancer drugs are needed, and modeling can assist in this endeavor. This paper describes classification models that were constructed to predict which fixed-ratio mixtures created from a pool of 10 drugs would show a high degree of in-vitro synergism against H460 human lung cancer cells. One of the tested drugs was doxorubicin and the others wer...

A database of about 700 high-resolution kinase structures was used to test the reliability of 17 docking procedures (using six docking software packages) by means of self- and cross-docking studies. The analysis of about 80 000 docking calculations suggests that the docking of an unknown ligand into a kinase has a probability of only 30-37% to be a correct ligand pose. However, based on the hyp...

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 ...

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...

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 ...

Cross-docking is a warehousing strategy in logistics used by process industries making products with high proportions of distribution costs. It is described as the process of moving goods from suppliers to customers through a cross-dock terminal without a long-term storage in this facility. The vehicle routing problem with cross-docking (VRPCD) consists of fulfilling a set of transportation req...

Cross-linking in combination with mass spectrometry can be used as a tool for structural modeling of protein complexes and multidomain proteins. Although cross-links represent only weak structural constraints, the combination of a limited set of experimental cross-links with molecular docking/modeling is often sufficient to determine the structure of a protein complex or multidomain protein at ...

Protein-protein interactions play a key part in most biological processes and understanding their mechanism is a fundamental problem leading to numerous practical applications. The prediction of protein binding sites in particular is of paramount importance since proteins now represent a major class of therapeutic targets. Amongst others methods, docking simulations between two proteins known t...