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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
Fri Mar 13 2020
Journal Name
Sustainability
Consumers’ Perceptions and Attitudes toward Products Preventing Microfiber Pollution in Aquatic Environments as a Result of the Domestic Washing of Synthetic Clothes
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Microfibers released by synthetic clothes have a significant negative effect on the environment. Several solutions have been proposed and evaluated for their effectiveness, but studies have failed to address the human-centered aspects of these products. In this research, the possibilities and needs from a consumer perspective for a new filtering system for domestic washing machines were examined. First, a quantitative (questionnaire) and a qualitative (interviews and observations) exploration were done to understand the desired requirements from a user perspective. Next, the acceptance of various existing solutions for microfiber catching was investigated. To verify these requirements, a new concept was designed and evaluated with a

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Publication Date
Sat Nov 22 2025
Journal Name
Journal Of Baghdad College Of Dentistry
An Assessment of Oral Health in Hypertensive Patients Treated with HMG-CoA Reductase Inhibitors (Statins)
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Background: Hypertension is a chronic medical condition in which the blood pressure in the arteries is elevated, it's classified as either primary (essential) hypertension or secondary hypertension, and it increases the risk of ischemic heart disease, peripheral vascular disease and other cardiovascular diseases. Several classes of medications collectively referred to as antihypertensive drugs like beta blockers, calcium channel blockers, angiotensin converting enzyme (ACE) inhibitors, angiotensin receptor blockers, renin inhibitors and statins (HMG-CoA) reductase inhibitor. Statin medication may have some beneficial effects when subjects have dental plaque or signs of periodontitis as gingival bleeding. The purpose of this study were to as

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Publication Date
Sun Dec 15 2019
Journal Name
Al-adab Journal
La faculté articulatoire de l'apprenant irakien Dans une classe de français langue étrangère A l’université de Bagdad Etude comparative
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Publication Date
Thu Sep 01 2016
Journal Name
Journal Of Engineering
The Effect of Vehicle Body Shapes on the Near Wake Region and Drag Coefficient: A Numerical Study
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The purpose of this paper is to gain a good understanding about wake region behind the car body due to the aerodynamic effect when the air flows over the road vehicle during its movement. The main goal of this study is to discuss the effect of the geometry on the wake region and the aerodynamic drag coefficient. Results will be achieved by using two different shapes, which are the fastback and the notchback. The study will be implemented by the Computational Fluid Dynamic (CFD) by using STAR-CCM+® software for the simulation. This study investigates the steady turbulent flow using k-epsilon turbulence model. The results obtained from the simulation show that the region of the air separation behind the vehicle

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Publication Date
Mon Dec 21 2020
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
COMPARATIVE STUDY OF SEVERAL MORPHOLOGICAL AND REPRODUCTIONAL ASPECTS FOR SOME SPECIES OF THE BELLEVALIA LAPEYROUSE, 1808 AND ORNITHOGALUM LINNAEUS, 1753 (ASPARAGALES, ASPARAGACEAE) IN CENTRAL AND NORTH OF IRAQ
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This study aims to study some morphological and reproductional characteristics in eleven species of two genera belonging to the family of Asparagaceae, which are Bellevalia Lapeyrouse, 1808 and Ornithogalum Linnaeus, 1753 and the species are: Bellevalia chrisii Yildirim and Sahin, 2014; Bellevalia flexuosa Boissier, 1854; Bellevalia kurdistanica Feinbrun, 1940; Bellevalia longipes Post, 1895; Bellevalia macrobotrys Boissier, 1853; Bellevalia paradoxa Boissier, 1882; Bellevalia parva Wendelbo, 1973; Bellevalia saviczii Woronow, 1927; Ornithogalum brachystachys C. Koch, 1849; Ornithogalum neurostegium Boissier, 1882 and Ornithogalum pyrenaicum Linnaeus, 1753. These species were identified and compared with each other; the results showed th

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Publication Date
Sun Sep 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Measurement of economic returns and environmental and social for green sector trade A prospective study in institutions of Basra to focus on the electricity sector
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        Environmental risk growing Become challenge "and a matter of controversy and concern to many of those concerned with environment, social, economic, and the same happens with the administrative rather than in isolation for this movement, as the issues of climate change Disturbed and troubled him, especially after what caused the risk of destruction, and irresponsibility , chaos, and the futility of resources, crops, fields,  nature and homes and reactors, and after what happened in Japan from the scourge of "Hurricane tsunami " and earthquakes successive accompanied him and what became of him by surprise catastrophic affected the economy and the univ

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Publication Date
Sat Aug 01 2020
Journal Name
Heat Transfer
A parametric study of a photovoltaic panel with cylindrical fins under still and moving air conditions in Iraq
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Publication Date
Fri Mar 15 2024
Journal Name
Journal Of Baghdad College Of Dentistry
A clinicopathological analysis of 151 odontogenic tumors based on new WHO classification 2022: A retrospective cross-sectional study
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Background: Odontogenic tumors are a diverse group of lesions with a variety of clinical behavior and histopathologic subtypes, from hamartomatous and benign to malignant. The study aimed to examine the clinical and pathological features of odontogenic tumors in Baghdad over the last 11 years (2011–2021). Materials and Methods: The present retrospective study analyzed all formalin-fixed, paraffin-embedded tissue blocks of patients diagnosed with an odontogenic tumor that were retrieved from archives at a teaching hospital/College of Dentistry in Baghdad University, Iraq, between 2011 and 2021. The diagnosis of each case was confirmed by examining the hematoxylin and eosin stained sections by two expert pathologists. Data from pati

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Publication Date
Sat Dec 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Organizational Tactics An Approach to Strategic Agility A field study in a sample of mobile operators in Iraq
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The current research dealt with the issue of organizational skillfulness as an entry point to reach strategic agility. The study has been tested in Iraq's mobile operators - Asia Cell, Zain Iraq and Cork Telecom. The study was applied to a sample of (93) managers distributed at various levels of management (board members, general managers, commissioners, department managers, people managers, unit managers, office managers). The survey used the questionnaire as a key tool for collecting data and information as well as personal interviews. It has sought to test a number of hypotheses related to correlation and influence relationships between the variables of the study, in order to answer the questions related to the problem of stud

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Publication Date
Mon Dec 03 2018
Journal Name
Journal Of Engineering
Comparative Analysis of Various Multicarrier Modulation Techniques for Different Multilevel Converters
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The applications of Multilevel Converter (MLC) are increased because of the huge demand for clean power; especially these types of converters are compatible with the renewable energy sources. In addition, these new types of converters have the capability of high voltage and high power operation. A Nine-level converter in three modes of implementation; Diode Clamped-MLC (DC-MLC), Capacitor Clamped-MLC (CC-MLC), and the Modular Structured-MLC (MS-MLC) are analyzed and simulated in this paper. Various types of Multicarrier Modulation Techniques (MMTs) (Level shifted (LS), and Phase shifted (PS)) are used for operating the proposed Nine level - MLCs. Matlab/Simulink environment is used for the simulation, extracting, and ana

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