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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
Sat Dec 30 2023
Journal Name
Journal Of Economics And Administrative Sciences
Financial Variables and Their Effects on The Development of Bank Credit and Productive Sectors in Iraq Using a Path Analysis Model
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This study aims to measure and analyze the direct and indirect effects of the financial variables, namely (public spending, public revenues, internal debt, and external debt), on the non-oil productive sectors with and without bank credit as an intermediate variable, using quarterly data for the period (2004Q1–2021Q4), converted using Eviews 12. To measure the objective of the study, the path analysis method was used using IBM SPSS-AMOS. The study concluded that the direct and indirect effects of financial variables have a weak role in directing bank credit towards the productive sectors in Iraq, which amounted to (0.18), as a result of market risks or unstable expectations in the economy. In addition to the weak credit ratings of borr

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Publication Date
Sat Aug 16 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Periodontal health status of heavy and light smokers and its correlation with salivary superoxide dismutase enzyme (A comparative study)
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Background: Periodontal disease is a chronic bacterial infection that affects the gingiva and bone supporting the teeth. Smoking, which is an important risk factor for periodontitis, induce oxidative stress in the body and cause an imbalance between reactive oxygen species (ROS) and antioxidants, such as superoxide dismutase (SOD). This study aimed to evaluate the influence of smoking on periodontal health status by estimating the levels of salivary SOD level in non-smokers (controls) and light and heavy smokers and to test the correlation between the SOD enzyme level and the clinical periodontal parameters in each group. Materials and Methods: The study sample consisted of 75 male, with age ranged from 35 to 50 years. Clinically, the perio

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Publication Date
Sat Aug 16 2025
Journal Name
Journal Of Baghdad College Of Dentistry
An Assessment of Salivary Leptin and Resistin Levels in Type Two Diabetic Patients with Chronic Periodontitis (A Comparative Study)
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Background: Type 2 diabetes mellitusand chronic periodontitis hold a close relationship that has been the focus of many researches. Currently there is an appreciation to the role of adipose tissue-derived substances "the adipokines" in immune-inflammatory responses; also, there is an interest in using the simple non-invasive saliva in diagnosing and linking oral and general health problems. The current study aims to determine the periodontal health status in the chronic periodontitis patients with and without poorly or well controlled type 2 diabetes mellitus, measure the salivary levels of two adipokines "leptin and resistin", pH and flow rate and then correlate between these clinical periodontal, biochemical and physical parameters in eac

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Publication Date
Mon Aug 03 2020
Journal Name
Rawal Medical Journal
Surgical fixation and grafting of traumatic distal tibia atrophic nonunion with or without platelet-rich plasma: A comparative study
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Objective: To compare distal tibia nonunion plating and grafting with and without platelet-rich plasma (PRP) regarding union rate, union time and complications Conclusion: Combining PRP with autologous bone graft results in a higher union rate, less healing duration, less post-operative pain, and more callus formation. (Rawal Med J 202;45:629- 632). Methodology: In this prospective comparative study, 32 patients with nonunion tibia from July 2017 January 2019 were divided into two groups: group A (16 cases) were treated by plating and grafting with PRP and group B (16 cases) were treated by plating and grafting only. Keywords: Tibial nonunion, bone graft, plateletrich plasma. Results: There was higher union rate in group A related to group

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Publication Date
Mon Jun 08 2020
Journal Name
Research Journal Of Chemistry And Environment
High Performance Liquid Chromatographic and Areaunder Curve spectrophotometric Methods forEstimation of Cefixime in Pure and MarketedFormulation: A Comparative Study
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Cefixime is an antibiotic useful for treating a variety ofmicroorganism infections. In the present work, tworapid, specific, inexpensive and nontoxic methods wereproposed for cefixime determination. Area under curvespectrophotometric and HPLC methods were depictedfor the micro quantification of Cefixime in highly pureand local market formulation. The area under curve(first technique) used in calculation of the cefiximepeak using a UV-visible spectrophotometer.The HPLC (2nd technique) was depended on thepurification of Cefixime by a C18 separating column250mm (length of column) × 4.6 mm (diameter)andusing methanol 50% (organic modifier) and deionizedwater 50% as a mobile phase. The isocratic flow withrate of 1 mL/min was applied, the temper

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Publication Date
Fri Jul 01 2022
Journal Name
Nternational Journal Of Special Education
Comparative Study between a Combination of Plants Extracts and Drugs on Thyroid Hormones and Lipid Profile in Experimental Animals
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The thyroid gland is a vital part of the overall endocrine system, which is regulated some of body function as oxygen use, basal metabolic rate, growth, cellular metabolism and development This study shed light on a number of extracts that have been shown to have beneficial effects on the thyroid and its function, as well as the various factors linked to thyroid dysfunction. The experiment was conducted to determine the effect of a mixture of two extracts of "Fucus vesiculosus (150 mg/ kg) with Coleus forskohlii (1000 mg/ kg) and Rosmarinus officinalis (220 mg/ kg) with Camellia sinensis (1.25 mg/ kg)" on thyroid hormones as well as lipids profile and tested the effectiveness of two drugs one of them stimulates the hormones of the thyroid (

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Publication Date
Thu Dec 31 2020
Journal Name
Indian Journal Of Public Health Research & Development
A Comparative Study of Vitamin D Levels and Some Biochemical Parameters between Healthy and Breast Cancer in Iraqi Females.
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Breast cancer is one of the most widespread cancers,depending on World Health Organization, cancer calculated for approximately 7.6 million incidences in 2008, whoever expected elevation in incidence is about 13.1 million in 2030. So that the current research investigates vitamin D role in the occurrence of this disease and explains if vitamin D has a positive effect on the incidence of disease, as well as measuring parathyroid hormone and estrogen levels. Three groups were included in this analysis: control healthy women, benign and malignant breast tumor women. All cases that were selected at the beginning of the disease diagnosis. According to statistical values vitamin D showed highly significant (P<0.001) decrease in benign (3.74±2.33

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Publication Date
Fri Nov 20 2020
Journal Name
Solid State Technology
Comparative Study for Bi-Clustering Algorithms: Historical and Methodological Notes
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Publication Date
Tue Mar 31 2015
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Performance of Corrosion Inhibitors Blend for Simulated Industrial Cooling Waters under Dynamic Conditions
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   The inhibitive action of a blend of sodium nitrite/sodium hexametaphosphate (SN+SHMP) on corrosion of carbon steel in simulated cooling water systems (CWS) has been investigated by weight loss and electrochemical polarization technique. The effect of temperature, velocity, and salts concentrations on corrosion of carbon steel were studied in the absence and presence of mixed inhibiting blend. Also the effect of inhibitors blend concentrations (SN+SHMP), temperatures, and rotational velocity, i.e., Reynolds number (Re) on corrosion rate of carbon steel were investigated using Second-order Rotatable Design (Box-Wilson Design) in performing weight loss and corrosion potential approach. Electrochemical polarization measurements

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Publication Date
Mon Jan 01 2024
Journal Name
Journal Of Applied Pharmaceutical Science
The role of angiotensin converting enzyme (insertion)/(deletion) and angiotensin II type 1 receptor (A1166C) gene polymorphisms in antiproteinuric effect of ACE inhibitors in type 2 diabetic Iraqi patients
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The angiotensin converting enzyme (ACE) I\D gene polymorphism influences the blood ACE enzyme activity. Renoprotective effect of ACE inhibitors (ACEIs) varies among patients due to genetic variation, particularly in Renin-Angiotensin-Aldosterone System genes. This study investigates the genetic variations of ACE I\D and AGT1RA1166C gene polymorphisms in the antiproteinuric effect of ACEI therapy in type 2 diabetes mellitus (T2DM) patients. This is a cross-sectional study that included 76 T2DM patients who are ACEI users, divided into two groups: T2DM without diabetic kidney disease (DKD) included 31 patients, and T2DM with DKD included 45 patients. Urine samples were taken for measurement of urine albumin and creatinine, then calcul

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