Integrating Dock-Door Assignment and Vehicle Routing in Cross-Docking

The necessity of treating receptor flexibility in proteinligand docking has been widely acknowledged and is the subject of extensive research in the field of drug discovery [1]. The use of multiple discrete protein conformations, so-called ensemble docking, has been proven to be a valid concept to mimic target plasticity in docking experiments [2,3]. Using molecular dynamics (MD) the number of ...

One of the most important factors in implementing supply chain management is to efficiently control the physical flow of the supply chain. Due to its importance, many companies are trying to develop efficient methods to increase customer satisfaction and reduce costs. In various methods, cross-docking is considered a good method to reduce inventory and improve responsiveness to various customer...

Stress-specific activation of the chaperone Hsp33 requires the unfolding of a central linker region. This activation mechanism suggests an intriguing functional relationship between the chaperone's own partial unfolding and its ability to bind other partially folded client proteins. However, identifying where Hsp33 binds its clients has remained a major gap in our understanding of Hsp33's worki...

Dilated cardiomyopathy is a disease of left ventricular dysfunction accompanied by impairment of the β1-adrenergic receptor (β1-AR) signal cascade. The disturbed β1-AR function may be based on an elevated sympathetic tone observed in patients with heart failure. Prolonged adrenergic stimulation may induce metabolic and electrophysiological disturbances in the myocardium, resulting in tachyarrhy...

In order to improve docking score correction, we developed several structure-based quantitative structure activity relationship (QSAR) models by protein-drug docking simulations and applied these models to public affinity data. The prediction models used descriptor-based regression, and the compound descriptor was a set of docking scores against multiple (∼600) proteins including nontargets. Th...

Existing flexible docking approaches model the ligand and receptor flexibility either separately or in a loosely coupled manner, which captures the conformational changes inefficiently. Here, we propose a flexible docking approach, MedusaDock, which models both ligand and receptor flexibility simultaneously with sets of discrete rotamers. We developed an algorithm to build the ligand rotamer li...

Supply chains are going to evolve by a new technology, which is called the Electronic Product Code (EPC) technology, based on radio frequency identification (RFID). This provides new opportunities in automatic identification that none of previous technologies offered. It also appears to have the potential to enhance Efficient Consumer Response (ECR), which is a grocery industry supply chain man...

ATP is involved in numerous biochemical reactions in living cells interacting with different proteins. Molecular docking simulations provide considerable insight into the problem of molecular recognition of this substrate. To improve the selection of correct ATP poses among those generated by docking algorithms we propose a post-docking reranking criterion. The method is based on detailed analy...

We study the quality ranking of different information structures. In a unified setting, we present eight representations of essentially the same notion that may arise in distinct literatures, and also establish the intricate relationships among them. The forms that are less familiar to researchers turn out to be more relevant to the operations management context. We also relate the information ...