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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
Solving Time-Cost Tradeoff Problem with Resource Constraint Using Fuzzy Mathematical Model
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Scheduling considered being one of the most fundamental and essential bases of the project management. Several methods are used for project scheduling such as CPM, PERT and GERT. Since too many uncertainties are involved in methods for estimating the duration and cost of activities, these methods lack the capability of modeling practical projects. Although schedules can be developed for construction projects at early stage, there is always a possibility for unexpected material or technical shortages during construction stage. The objective of this research is to build a fuzzy mathematical model including time cost tradeoff and resource constraints analysis to be applied concurrently. The proposed model has been formulated using fuzzy the

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Publication Date
Sun Mar 01 2009
Journal Name
Baghdad Science Journal
A Study of structural and electrical properties ofCuIn (Sex Te1-x) 2 thin films
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structural and electrical of CuIn (Sex Te1-x)2

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Publication Date
Thu Jun 27 2019
Journal Name
Molecular Crystals And Liquid Cryst
A New Series of Triazine-core Based Mesogenic Derivatives: Synthesis, Characterization and Mesomorphic Study
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The synthesis, characterization and mesomorphic properties of two new series of triazine-core based liquid crystals have been investigated. The amino triazine derivatives were characterized by elemental analysis, Fourier transforms infrared (FTIR), 1HNMR and mass spectroscopy. The liquid crystalline properties of these compounds were examined by differential scanning calorimetry (DSC) and polarizing optical microscopy (POM). DSC and POM confirmed nematic (N) and columnar mesophase textures of the materials. The formation of mesomorphic properties was found to be dependent on the number of methylene unit in alkoxy side chains.

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Publication Date
Sun Jun 12 2011
Journal Name
Baghdad Science Journal
A Study of Wear Rate Epoxy Resin filled with SiO2 particle and Glass fibers
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This research is devoted to study the effect of different in weight percentage of Sio2 particles and glass fibers (5, 10, 15, 20) wt. % on the wear rate epoxy resin. The results show that the value of hardness increase with the increase for the weight percentage of reinforcing particles and fibers, while the wear rate decrease with the increase the load level of the reinforcing particles and fibers . The largest value of the hardness, and the lowest value of the wear rate for epoxy reinforced with 20% of SiO2, the wear rate increase in general with increasing the applied load.

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Publication Date
Sun Mar 01 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Interleukine-6 Level in Saliva of Patients with Chronic Periodontitis: A Case-Control Study
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Background:Periodontal diseases are infectious diseases in which periodontalpathogens trigger chronic inflammatory and immune responses. Interleukine-6 is a multifunctional cytokine playing a central role in inflammation and tissue injury.The aim of the study IS to determine the level of Interleukin-6(IL-6) in saliva of patients with chronic periodontitis compared to healthy subjects. Materials and Methods:The total subjects of the present study is 60, divided into 3 groups; 20 patients with chronic periodontitis with pocket depth(PD ≥4 mm)(group I), 20 patients with pocket depth(PD <4 mm) with clinical attachment loss (group II), and 20 healthy controls with pocket probing depth (PPD ≤ 3 mm) without clinical attachment loss (g

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Publication Date
Sun Jun 05 2016
Journal Name
Baghdad Science Journal
Synthesis and Characterization of Cu(I)-Folic Acid Complex A Theoretical and Experimental Study
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Copper (I) complex containing folic acid ligand was prepared and characterized on the basis of metal analyses, UV-VIS, FTIR spectroscopies and magnetic susceptibility. The density functional theory (DFT) as molecular modeling calculations was used to determine the donor atoms of folic acid ligand which appear clearly at oxygen atoms binding to hydrogen. Detection of donation sights is supported by theoretical parameters such as geometry, mulliken population, mulliken charge and HOMO-LUMO gap obtained by DFT calculations.

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Publication Date
Sun Dec 01 2019
Journal Name
Baghdad Science Journal
Adsorption of Some Alephatic Dicarboxylic Acids on Zinc Oxide: A kinetic and Thermodynamic Study
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The adsorption of Malonic acid, Succinic acid, Adipic acid, and Azelaic acid from their aqueous solutions on zinc oxide surface were investigated. The adsorption efficiency was investigated using various factors such as adsorbent amount, contact time, initial concentration, and temperature. Optimum conditions for acids removal from its aqueous solutions were found to be adsorbent dose (0.2 g), equilibrium contact time (40 minutes), initial acids concentration (0.005 M). Variation of temperature as a function of adsorption efficiency showed that increasing the temperature would result in decreasing the adsorption ability. Kinetic modeling by applying the pseudo-second order model can provide a better fit of the data with a greater correla

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Publication Date
Mon Sep 01 2025
Journal Name
Journal Of Language Teaching And Research
A Pragmatic Study of Nonverbal Communication in Johnny Depp Versus Amber Heard’s Public Trial
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Depp and Heard's trial has reaped significant attention due to the domestic violence allegations directed towards each other. This paper sheds light on the repressed narrative beyond the mere words spoken aloud. It delves into an overlooked aspect, i.e., nonverbal communication. Previous studies focused on one or two categories of nonverbal communication. Therefore, the current study investigates the types and sub-types of nonverbal communication exhibited by both rivals within the courtroom setting. To examine the credibility and repressibility of nonverbal communication, the researchers have carefully watched (28) videos representing the whole trial's event. Some nonverbal communication was traced through the whole (28) videos fro

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Publication Date
Mon Jul 23 2018
Journal Name
Journal Of Clinical Nursing
Factors influencing nurses’ knowledge acquisition of diabetes care and its management: A qualitative study
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Aim

To identify and explore the factors nurses perceive as influencing their knowledge acquisition in relation to diabetes care and its management in Saudi Arabia.

Background

Diabetes continues to pose major healthcare challenges despite advances in diabetes management. Nurses have a crucial role in diabetes care, but diabetes knowledge deficits deter effective collaboration with other healthcare providers in educating patients about diabetes self‐management.

Design

An exploratory descriptive qualitative design.

Method
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Publication Date
Mon Feb 28 2022
Journal Name
Structural Chemistry
Sensitivity of SnO2 nanoparticles/reduced graphene oxide hybrid to NO2 gas: A DFT study
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Abstract<p>The sensitivity of SnO<sub>2</sub> nanoparticles/reduced graphene oxide hybrid to NO<sub>2</sub> gas is discussed in the present work using density functional theory (DFT). The SnO<sub>2</sub> nanoparticles shapes are taken as pyramids, as proved by experiments. The reduced graphene oxide (rGO) edges have oxygen or oxygen-containing functional groups. However, the upper and lower surfaces of rGO are clean, as expected from the oxide reduction procedure. Results show that SnO<sub>2</sub> particles are connected at the edges of rGO, making a p-n heterojunction with a reduced agglomeration of SnO2 particles and high gas sensitivity. The DFT results are in</p> ... Show More
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