7 ABSTRACT: Although many popular docking programs 8 include a facility to account for covalent ligands, large-scale 9 systematic docking validation studies of covalent inhibitors have 10 been sparse. In this paper, we present the development and 11 validation of a novel approach for docking and scoring covalent 12 inhibitors, which consists of conventional noncovalent docking, 13 heuristic for...

Existing self-reconfigurable robots achieve connections and disconnections by a separate drive of the docking system. In this paper, we present a new docking system with which the connections and disconnections are driven by locomotion actuators, without the need for a separate drive, which reduces the weight and the complexity of the modules. This self-reconfigurable robot consists of two type...

BACKGROUND Neuroblastoma (NB) is a childhood cancer causing significant mortality in at least 1% children worldwide. NB is an embryonically derived tumor. The causative agents include genetic predisposition and dysregulated signaling cascades. Survivin is an important anti-apoptotic protein that is significantly up-regulated in NB. In this study, a naturally occurring ligand - Piperine was asse...

because of participation in many aspects of human life, and due to oxidation-sensitive characteristics of dopamine (da) and arachidonoyl dopamine (aa-da), the necessity of biocompatible carrier to keep them against oxidation is of importance. in this work, we explored the putative binding sites of da and aa-da to -lactoglobulin (blg) as potent carrier. docking results identified the binding si...

inhibitors of soluble epoxide hydrolase (seh) represent one of the novel pharmaceutical approaches for treating hypertension, vascular inflammation, pain and other cardiovascular related diseases. most of the potent seh inhibitors reported in literature often suffer from poor solubility and bioavailability. toward improving pharmacokinetic profile beside favorable potency, two series of 4-benza...

in the current study, both ligand-based molecular docking and receptor-based quantitative structure activity relationships (qsar) modeling were performed on 35 diaryl urea derivative inhibitors of v600e b-raf. in this qsar study, a linear (multiple linear regressions) and a nonlinear (partial least squares least squares support vector machine (pls-ls-svm)) were used and compared. the predictive...

BACKGROUND Hymenodictyon excelsum is a medicinal plant traditionally used for tumor treatment as it contains phytochemicals of anthraquinone and coumarin class. OBJECTIVES The aim of the present study was to unfold the therapeutic value of selected phytocompounds of Hymenodictyon excelsum in prostate cancer. MATERIALS AND METHODS Eight phytochemicals were selected based on the literature se...

Ligand-protein docking is increasingly used in Drug Discovery. The initial limitations imposed by a reduced availability of target protein structures have been overcome by the use of theoretical models, especially those derived by homology modeling techniques. While this greatly extended the use of docking simulations, it also introduced the need for general and robust criteria to estimate the ...

Protein tyrosine kinases (PTK) are key enzymes of mammalian signal transduction. For the fidelity of signal transduction, each PTK phosphorylates only one or a few proteins on specific Tyr residues. Substrate specificity is thought to be mediated by PTK-substrate docking interactions and recognition of the phosphorylation site sequence by the kinase active site. However, a substrate-docking sit...

The importance of understanding interactomes makes preeminent the study of protein interactions and protein complexes. Traditionally, protein interactions have been elucidated by experimental methods or, with lower impact, by simulation with protein docking algorithms. This article describes features and applications of the BiGGER docking algorithm, which stands at the interface of these two ap...