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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
Wed Mar 18 2020
Journal Name
Baghdad Science Journal
A Comparative Study of Heavy Metals and Trace Elements Concentration in Milk Samples Consumed in Iraq
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The measurements of major and trace elements in different brands of milk powder selected from the Iraqis market via the X-ray fluorescence (XRF) Technique have been studied in the present work. The result of the measurements reveals the high concentrations of sodium, phosphorus, sulfur, chlorine, potassium, calcium and magnesium. Furthermore, low concentrations of aluminum, silicon, iron, bromine, molybdenum, iodine, barium, titanium, manganese, cobalt, chrome, nickel, copper, zinc and lead were detected. Neutron activation analysis (NAA) and Kjeldahl technique were also employed to determine the concentrations of nitrogen. It was found that the nitrogen concentration was in the range of (1.96 - 3.23) % which is within the permissible li

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Publication Date
Tue Jul 22 2025
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Effectiveness of Intralesional Vitamin D and Bleomycin Injections in Treating Recalcitrant Plantar Wart: A Comparative Study
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Background: Intralesional injections of vitamin D and bleomycin have gained growing clinical interest in the treatment of recalcitrant plantar warts, with pain as a major limitation associated with their use. Objective: To assess the clinical outcomes of vitamin D and bleomycin in managing treatment-resistant plantar warts. Methods: An interventional comparative study conducted on patients diagnosed with recalcitrant plantar warts over 9 months and not treated for two months. Patients were divided randomly into two groups: group A (24 patients received intralesional vitamin D) and group B (24 patients received intralesional bleomycin). The clearance rate and pain score were estimated by visual analogue scale (VAS). Results: 48 patie

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Publication Date
Tue Oct 09 2018
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
A COMPARATIVE HISTOLOGICAL STUDY OF THYROID TISSUE IN CARP FISH CYPRINUS CARPSIO AND MICE SWISS ALBICANS
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    This histological study was carried out to compare between the thyroid gland of mice (as a model of the mammals) and the thyroid tissue of fish.  Unlike mice, the thyroid gland of fish can't be recognized by naked eye.  The present study revealed that the thyroid of mice varied from that of fish by the location and the histological structure. The study classified the physiological state of the thyroid of mice into three states and that of the fish into only two states. Accordingly, the study concluded that the metabolism of thyroid fish was of moderate type.

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Publication Date
Sat Oct 19 2024
Journal Name
Mustansiriyah Journal Of Sports Science
Traditional Championships sports (Zurkhaneh and Sumo): a comparative historical study of historical origins and traditional rituals
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Many societies have some sports that play a pivotal role in enhancing human physical strength and martial arts and preserving religious values and beliefs. The most prominent of these traditional heroic sports are Zurkhaneh and Sumo, two sports that have their historical origins in the Iranian and Japanese cultural heritage. The research aims at shed light on the historical origins, symbolic rituals, and traditional elements of the sports of Zurkhaneh and Sumo, and to highlight the distinctive characteristics of the sports of Zurkhaneh and Sumo through objective analysis and comparison. The methodology used in this research is the historical approach, using the method of comparative analysis. This method includes analyzing information deriv

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Publication Date
Mon Jan 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
Grammatical Behaviour and Uses of Negative and Prohibitive Particles in Semitic Languages: A Comparative Semitic Study
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      Grammatical particles are so important in understanding a text and its meaning in linguistic context. This paper  " Grammatical Behavior and Uses of Negative and Prohibitive Particles in Semitic Languages: A Comparative Semitic Study"

      tackles  a very important topic in Semitic languages. Comparative studies in Semitic languages shed light on  phenomena in different languages that are related or have one common origin. No doubt, such studies have their own effects on language study in general especially when studying a specific phenomenon and explaining it by reliance on the one origin, or by investigating the various phases of its historical development.

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Publication Date
Thu Mar 25 2021
Journal Name
International Journal Of Drug Delivery Technology
A comparative study of retinol-binding protein-4 and progranulin in iraqi women with thyroid disorder
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Thyroid hormones (TH) regulate the metabolic processes required for normal development and growth; also, to organizemetabolism in adults, any defect in thyroid function leads to abnormality in thyroid hormones level. The current study hasbeen designed to find the relationship between retinol-binding protein-4 and progranulin in the serum of Iraqi women withhypothyroidism and hyperthyroidism, also, to study whether these patients are exposed to a risk of developing diabetes mellitus,and PGRN may be a biomarker in detection early stage of diabetes mellitus.Materials and Methods: in this study, serum samples were obtained from 50 Iraqis women patients, [25 patients withhypothyroidism (G2) and 25 patients with hyperthyroidism (G3)] in addition

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Publication Date
Mon Mar 15 2021
Journal Name
Al-academy
Semiotics of Musical Sign in Iraqi Pantomime Show (Ahriman) as a Model: علي عدي صاحب-شيماء حسين طاهر
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The musical sign was associated with the first appearances of acting that are based on human gestures and expressive and silent movements, and they contributed in accentuating and clarifying these gestures and explain their meanings and indications, and they remained with them until these gestures turned into artistic theatrical shows so that the musical sign would have many functions and constitute the main pillars for this kind of show.
The musical sign is a language not much different than the human language in the semiotic analysis. There has been an increased interest in it and its use in the mime shows by the graduates who realized its necessity and significance in the pantomime show intellectually, artistically and aesthetical

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Publication Date
Thu Dec 15 2022
Journal Name
Al-academy
The controversy of aesthetic interpretation between the sculptures and their titles Contemporary Iraqi Sculpture "Experiments in Contemporary Iraqi Sculpture Exhibition as a Model"
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The research tagged with the controversy of aesthetic interpretation between the sculptures and their titles in contemporary Iraqi sculpture, “Exhibition of Experiments in Contemporary Iraqi Sculpture as a Model”, and it is one of the new research that contributes to strengthening the critical path in the Iraqi fine movement, as the first chapter dealt with the research problem stemming from the question: What is the impact of the aesthetic hermeneutic controversy between the title and the title in contemporary Iraqi sculpture?, and do the titles of the sculptural works help to understand or enhance their contents?, The research objective included: To identify the controversy of the aesthetic interpretation of sculptures and their ti

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Publication Date
Sat Jun 01 2024
Journal Name
Materials And Structures
Exploring the efficacy of sawdust ash as a mineral filler substitute for the production of asphalt mixtures
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Many waste materials can be repurposed effectively within asphalt concrete to enhance the performance and sustainability of pavement. One of these waste materials is sawdust ash (SDA). This study explores the beneficial use of SDA as a substitute for limestone dust (LD) mineral filler in asphalt concrete. The replacement rate was 0%, 15%, 30%, 45%, and 60% by weight of total mineral filler. Scanning electron microscopy (SEM) was employed to assess the surface morphology of Sawdust (SD), SDA, and LD. In addition, a series of tests, including Marshall stability and flow, indirect tensile strength,moisture susceptibility, and repeated uniaxial loading tests, were conducted to examine the performance characteristics of asphalt mixtures of diffe

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Publication Date
Thu Aug 01 2024
Journal Name
Misan Journal For Physical Education Sciences
A comparative study of the reasons for the reluctance of female physical education teachers in “Baqubah” to participate in refereeing sports competitions according to the variable of years of service
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When searching for an answer to the following question: What are the reasons for the reluctance of female physical education teachers in secondary schools to referee sports competitions according to the variable of years of service? It was found that the research aimed to reveal the differences between the opinions of the research sample of physical education teachers in secondary schools (girls) about refereeing sports competitions according to the variable of years of service. To achieve the research goal, it is assumed that there are significant differences between the average opinions of the research sample of female teachers and their reluctance and the reasons for the differences in the practice of refereeing sports competitions accor

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