This study addresses the pickup and delivery problem for cross-docking strategy, in which shipments are allowed to be transferred from suppliers to retailers directly as well as through cross-docks. Usual models that investigate vehicle routing in cross-docking networks force all vehicles to stop at the cross-dock even if a shipment is about to a full truckload or the vehicle collects and deliv...

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...

While organizing the cross-docking operations, cross-dock managers are confronted with many decision problems. One of these problems is the truck scheduling problem. This article presents a truck scheduling problem that is concerned with both inbound and outbound trucks at multiple dock doors. The objective is to minimize the total travel time and the total tardiness. The truck scheduling probl...

human immunodeficiency virus infection / acquired immunodeficiency syndrome (hiv/aids) is a disease pertained to the human immune system. given its crucial role in viral replication, hiv-1 protease (hiv-1 pr) is a prime therapeutic target in aids therapy. in this regard, the dynamic aspects of ligand-enzyme interactions may indicate an important role of conformational variability in hiv-1 pr in...

Ligand enrichment among top-ranking hits is a key metric of molecular docking. To avoid bias, decoys should resemble ligands physically, so that enrichment is not simply a separation of gross features, yet be chemically distinct from them, so that they are unlikely to be binders. We have assembled a directory of useful decoys (DUD), with 2950 ligands for 40 different targets. Every ligand has 3...

The inclusion of receptor flexibility in protein-ligand docking experiments has become a major research interest in drug discovery [1,2]. One of the possible methods applied is the use of multiple discrete protein conformations, so called ensemble docking [3,4]. With computational techniques like Molecular Dynamics (MD) a large number of different conformations can be generated, not all of whic...

The main complicating factor in structure-based drug design is receptor rearrangement upon ligand binding (induced fit). It is the induced fit that complicates cross-docking of ligands from different ligand-receptor complexes. Previous studies have shown the necessity to include protein flexibility in ligand docking and virtual screening. Very few docking methods have been developed to predict ...

Since determining the crystallographic structure of all peptide-MHC complexes is infeasible, an accurate prediction of the conformation is a critical computational problem. These models can be useful for determining binding energetics, predicting the structures of specific ternary complexes with T-cell receptors, and designing new molecules interacting with these complexes. The main difficultie...

Polyketides, a diverse group of heteropolymers with antibiotic and antitumor properties, are assembled in bacteria by multiprotein chains of modular polyketide synthase (PKS) proteins. Specific protein-protein interactions determine the order of proteins within a multiprotein chain, and thereby the order in which chemically distinct monomers are added to the growing polyketide product. Here we ...