This paper is designed to examine the binding behavior of Coumarin with bovine -casein (βCN) through fluorescence spectroscopy and molecular modeling techniques. The data analysis on fluorescence titration experiments at various temperatures represents the enthalpy driven nature for the formation of Coumarin–βCN complex and the prevailed role of hydrogen bonds and van der Waals interactions in...

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...

introduction : the innate immune system as the first line of defense against the pathogens recognizes pathogen-associated molecular patterns (pamps) by toll-like receptors (tlrs). interaction of bacterial pamps by tlrs results in activation of innate and acquired immunity. fimh adhesin, a minor component of type 1 fimbriae encoded by uropathogenic escherichia coli (upec) is a pamp of tlr4 that ...

Human epidermal growth factor receptor 2 (HER2) is a member of the epidermal growth factor receptor family having tyrosine kinase activity. Overexpression of HER2 usually causes malignant transformation of cells and is responsible for the breast cancer. In this work, the virtual screening, molecular docking, quantum mechanics and molecular dynamics methods were employed to study protein–ligand ...

Studying the interaction of pharmaceutical ionic liquids with human serum albumin (HSA) can help investigating whether or not ionic liquid formation can enhance pharmacological profile of the discrete ingredients. In this respect, in the present work, the interactions of Benzalkonium Ibuprofenate, as a well-known active pharmaceutical ionic liquid, Benzalkonium Chloride, and also Sodium Ibuprof...

The efficient and accurate quantification of protein-ligand interactions using computational methods is still a challenging task. Two factors strongly contribute to the failure of docking methods to predict free energies of binding accurately: the insufficient incorporation of protein flexibility coupled to ligand binding and the neglected dynamics of the protein-ligand complex in current scori...

Hsp90 is a major protein involved in the stabilization of various proteins in cancer cells. The present investigation focused on the molecular docking simulation studies of flavanols as inhibitors of Hsp90 at the high affinity adenosine triphosphate (ATP) binding site and analyzed absorption, distribution, metabolism, excretion and toxicity (ADME-toxicity). The molecular docking analysis reveal...

-We have designed an improved method for solving the embedding problem, which consists in generating molecular conformations satisfying prescribed distance restraints. The problem was broken up into smaller subproblems by carrying out separate embeddings of subsets of the original point set. The relative orientation of the subsets were then determined by an additional embedding and the final co...

We report all-atom molecular dynamics and replica exchange molecular dynamics simulations on the unbound human immunodeficiency virus type-1 (HIV-1) transactivation responsive region (TAR) RNA structure and three TAR RNA structures in bound conformations of, in total, approximately 250 ns length. We compare the extent of observed conformational sampling with that of the conceptually simpler and...

As the speed and payload of Wheeled Mobile Robots (WMRs) increases and the clearances between obstacles and docking error tolerances decreases, methods for reducing tracking errors become increasingly important for a successful application. In this paper techniques and results are presented for improved tracking control of a WMR through the generation and dynamic simulation of paths with and wi...