The docking complex is a molecular complex necessary for assembly of outer dynein arms (ODAs) on the axonemal doublet microtubules (DMTs) in cilia and flagella. The docking complex is hypothesized to be a 24-nm molecular ruler because ODAs align along the DMTs with 24-nm periodicity. In this study, we rigorously tested this hypothesis using structural and genetic methods. We found that the ODAs...

In this study we introduce a rescoring method to improve the accuracy of docking programs against mPGES-1. The rescoring method developed is a result of extensive computational study in which different scoring functions and molecular descriptors were combined to develop consensus and rescoring methods. 127 mPGES-1 inhibitors were collected from literature and were segregated into training and e...

BACKGROUND Tail biting is a common and serious welfare problem in pig production, causing large economical losses. Tail docking is performed routinely in most EU countries to reduce the tail biting risk. However, tail docking is painful, and does not prevent tail biting totally. The risk factors behind tail docking are multifactorial and most analyses are based on studies using biological or ep...

Ligand-based and structure-based drug screening methods were integrated for in silico drug development by combining the maximum-volume overlap (MVO) method with a protein-compound docking program. The MVO method is used to select reliable docking poses by calculating volume overlaps between the docking pose in question and the known ligand docking pose, if at least a single protein-ligand compl...

BACKGROUND Protein-based pharmacophore models are enriched with the information of potential interactions between ligands and the protein target. We have shown in a previous study that protein-based pharmacophore models can be applied for ligand pose prediction and pose ranking. In this publication, we present a new pharmacophore-based docking program PharmDock that combines pose sampling and r...

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 inhi...

Intermolecular binding underlies every metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow us to study the binding process. Haptic-based docking provides an immersive virtual docking environment where the user can interact with and guide the molecules to t...

cross docking is a logistic strategy that plays the role of a middle knot in distribution network in the provision process. in logistic part, inventory holding is considered as an important matter in managing costs. not only cross docking reduces the inventory holding cost, but it also reduces the cost of collecting received orders, transportation and duration of sending. the products, which ar...

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...