One important factor in supply chain management is to efficiently control the supply chain flows. Due to its importance, many companies are trying to develop efficient methods to increase customer satisfaction and reduce costs. Cross-docking is considered a good method to reduce inventory and improve responsiveness. The Vehicle Routing Problem with Cross-Docking and Time Windows (VRP-CD-TW) con...

We have developed a new tool for virtual database screening. This tool, referred to as the Generic Evolutionary Method for molecular DOCKing (GEMDOCK), combines an evolutionary approach and a new pharmacophore-based scoring function. The former integrates discrete and continuous global search strategies with local search strategies to speed up convergence. The latter simultaneously serves as th...

Introduction: Drugs are mainly delivered to the target tissues by plasma proteins, such as human serum albumin, in the human body. Practical information about the thermodynamic parameters of drugs and their stability can be obtained using simulation methods, such as molecular docking. Material & Methods: This study, investigated the molecular docking of human serum albumin with fluorouracil an...

BEAR (Binding Estimation After Refinement) is a computational method for structure-based virtual screening. It was set up as a post-docking processing tool for the refinement of ligand binding modes predicted by molecular docking programs and the accurate evaluation of free energies of binding. BEAR has been validated in a number of computational drug discovery applications. It performed well i...

In this work, we validate and analyze the results of previously published cross docking experiments and classify failed dockings based on the conformational changes observed in the receptors. We show that a majority of failed experiments (i.e. 25 out of 33, involving four different receptors: cAPK, CDK2, Ricin and HIVp) are due to conformational changes in side chains near the active site. For ...

OBJECTIVE The purpose of this study was to evaluate the microtensile strength of composite bonded to interpenetrating polymer network (IPN) or cross-linked glass fibre posts and to observe the failure modes by using light and scanning electron microscopy. METHODS Twenty posts containing IPN resin matrix and 20 posts containing cross-linked epoxy polymer matrix were used for testing. One half ...

Protein-small molecule docking algorithms provide a means to model the structure of protein-small molecule complexes in structural detail and play an important role in drug development. In recent years the necessity of simulating protein side-chain flexibility for an accurate prediction of the protein-small molecule interfaces has become apparent, and an increasing number of docking algorithms ...