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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
Mon Jan 28 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Managerial Skills and It`s Role in Strengthening the Competitive Edge of Companies: A Case Study in the General Company for Construction Industries
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This research tries to reveal how to manage and control the competitive edge for business by building managerial skills in various organizational levels. Our research aims at finding out the nature of various technical, human and in tellectual skills of a new president whose superiority is his competitive ness in the application field at general company for construe tioual  industriesand testing the surveyed minor and major changes through a questionnaire to collect information from officials. The sample was composed of (45) director. The data was analyzed  using some methods and statistical programs. The most prominent of these is (SPSS) that was used to extract the arithmetic mean, standard deviation, correlation coefficient

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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Zankoy Sulaimani - Part A
A Comparison Study on the Formation of Administrative and Leadership Policies for the Team and Individual Olympic Games in the Iraqi National Olympic Committee
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The planning for the formation of administrative policies and guidance through leadership are important things for managing administrative processes and sporting activities. As both contribute in the stability of the administrative conditions, and their development in the sport federations, whether they both were attentive about team and individual Olympic Games. The two researchers observe that, there is a variation in the correct way of application. Particularly in the formulation of administrative policies and leadership describing it as, modern management standards for both team and individual Olympic Games in the Iraqi National Olympic Committee. That led to cause a misconception and lack of clarity for some administrators of those uni

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Publication Date
Tue Jun 01 2010
Journal Name
Al-khwarizmi Engineering Journal
Land Use/Cover Change Analysis Using Remote Sensing Data: A Case Study, Zhengzhou Area, Henan Province, China
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In the last two decades, arid and semi-arid regions of China suffered rapid changes in the Land Use/Cover Change (LUCC) due to increasing demand on food, resulting from growing population. In the process of this study, we established the land use/cover classification in addition to remote sensing characteristics. This was done by analysis of the dynamics of (LUCC) in Zhengzhou area for the period 1988-2006. Interpretation of a laminar extraction technique was implied in the identification of typical attributes of land use/cover types. A prominent result of the study indicates a gradual development in urbanization giving a gradual reduction in crop field area, due to the progressive economy in Zhengzhou. The results also reflect degradati

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Publication Date
Mon Dec 24 2018
Journal Name
Civil Engineering Journal
Artificial Neural Network Model for the Prediction of Groundwater Quality
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The present article delves into the examination of groundwater quality, based on WQI, for drinking purposes in Baghdad City. Further, for carrying out the investigation, the data was collected from the Ministry of Water Resources of Baghdad, which represents water samples drawn from 114 wells in Al-Karkh and Al-Rusafa sides of Baghdad city. With the aim of further determining WQI, four water parameters such as (i) pH, (ii) Chloride (Cl), (iii) Sulfate (SO4), and (iv) Total dissolved solids (TDS), were taken into consideration. According to the computed WQI, the distribution of the groundwater samples, with respect to their quality classes such as excellent, good, poor, very poor and unfit for human drinking purpose, was found to be

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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Traditional and molecular methods for diagnosing bacterial meningitis in Erbil city, Iraq
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Bacterial meningitis is a leading cause of illness and death worldwide. It is crucial for clinical and public health care, as well as disease control, to identify the meningitis-causing agent promptly. Between June 2021-February 2022, a total of 100 cerebrospinal fluid (CSF) and blood samples were collected from suspected cases of meningitis admitted to Raparin Paediatric Teaching Hospital, Erbil city-Iraq. Cytochemical, cultural, and biochemical tests were conducted, and confirmed by molecular techniques. Bacterial culture findings were positive in 7% of CSF samples and just one positive among blood samples. The most common pathogens found by cultural characteristics and VITEK 2 Compact System were Staphylococcus sciuri in two

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Publication Date
Sat Apr 01 2023
Journal Name
Heliyon
A comprehensive review on modelling the adsorption process for heavy metal removal from waste water using artificial neural network technique
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Publication Date
Fri Jun 15 2018
Journal Name
Journal Of Baghdad College Of Dentistry
Periodontal health status of patients with Maxillary Chronic Rhinosinusitis (Part 1: Clinical study)
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Background: Periodontal diseases (PD) are inflammatory conditions of the tissues supporting the teeth, most often gingivitis and periodontitis. Maxillary chronic rhinosinusitis (MCRS) is the inflammation of the maxillary sinuses which is last for at least 12 consecutive weeks duration. Aims of study: Distribution of periodontal diseases among patients with Maxillary chronic rhinosinusitis according to gender and age. Materials and methods: Males and females subjects (25-45 years), divided into two groups; 150 patients suffer from MCRS and 130 subjects without MCRS. Clinical periodontal parameters; Plaque Index (PL.I), Gingival Index (G.I), Probing Pocket Depth (PPD), Clinical Attachment Level (CAL) and Bleeding On Probing (BOP) recorded f

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Publication Date
Fri Nov 01 2019
Journal Name
Journal Of Global Pharma Technology
Synthesis and Phase Transition Study of New Mesogence Derived from 1, 4-Phenylenediamine
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This work include synthesized and characterization the compound [I] by reaction 1,4-phenylenediamine with chloro acetic acid then this compound reaction with methanol in present sulfuric acid to synthesized ester compound [II] after that reaction with hydrazine hydrate to synthesized acide hydrazide [III] and the later compound reaction with substituted acetophenone[IV]n to synthesized substituted acetophenone hydrazones[V-XI]. In addition synthesized4-formylpyrazole derivatives [XIIXVIII] via cyclisation substituted acetophenone hydrazones [V-XI] with Vilsmeier-Haack reagent DMF/POCl3. The compounds characterized by melting points, FTIR, 1HNMR and mass spectroscopy. The mesomorphic behavior studied by using polarized optical microscopy and

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Publication Date
Mon Oct 02 2023
Journal Name
Journal Of Engineering
Controlling the Unbalanced Voltages of a Series-Connected Lead-Acid Batteries in a PV Power Storage System using Dynamic Capacitor Technique
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Lead-acid batteries have been used increasingly in recent years in solar power systems, especially in homes and small businesses, due to their cheapness and advanced development in manufacturing them. However, these batteries have low voltages and low capacities, to increase voltage and capacities, they need to be connected in series and parallel. Whether they are connected in series or parallel, their voltages and capacities must be equal otherwise the quality of service will be degraded. The fact that these different voltages are inherent in their manufacturing, but these unbalanced voltages can be controlled. Using a switched capacitor is a method that was used in many methods for balancing voltages, but their respons

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Publication Date
Wed Jun 03 2020
Journal Name
Journal Of Applied Mathematics
Order and Chaos in a Prey-Predator Model Incorporating Refuge, Disease, and Harvesting
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In this paper, a mathematical model consisting of a prey-predator system incorporating infectious disease in the prey has been proposed and analyzed. It is assumed that the predator preys upon the nonrefugees prey only according to the modified Holling type-II functional response. There is a harvesting process from the predator. The existence and uniqueness of the solution in addition to their bounded are discussed. The stability analysis of the model around all possible equilibrium points is investigated. The persistence conditions of the system are established. Local bifurcation analysis in view of the Sotomayor theorem is carried out. Numerical simulation has been applied to investigate the global dynamics and specify the effect

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