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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 Dec 21 2020
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
A CONTRIBUTION TO THE CHECKLIST OF THE JUMPING SPIDERS (ARANEAE: SALTICIDAE) OF ARMENIA
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The paper presents an annotated checklist of the Salticidae of Armenia. This study was carried out in 2019-2020 in order to provide an inventory of the Salticidae fauna. Thirteen species are reported for the Armenian fauna for the first time: Afraflacilla epiblemoides (Chyzer, 1891); Aelurillus v-insignitus (Clerck, 1757); Asianellus festivus (C. L. Koch, 1834); Heliophanus dubius C. L. Koch, 1835; Heliophanus kochii Simon, 1868; Heliophanus tribulosus Simon, 1868; Heliophanus curvidens (O. Pickard-Cambridge, 1872); Macaroeris nidicolens (Walckenaer, 1802); Pellenes diagonalis (Simon, 1868); Pellenes geniculatus (Simon, 1868); Pellenes seriatus (Thorell, 1875); Pellenes tripunctatus (Walckenaer, 1802) and Phlegra fasciata (Hahn, 1826).

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Publication Date
Tue Jun 30 2020
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
BUILD AN EFFICIENT INVESTMENT PORTFOLIO USING THE WILLIAM RATIO (EMPIRICAL STUDY) IN IRAQ STOCK EXCHANGE: BUILD AN EFFICIENT INVESTMENT PORTFOLIO USING THE WILLIAM RATIO (EMPIRICAL STUDY) IN IRAQ STOCK EXCHANGE
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ABSTRACT

            This study aimed to choose top stocks through technical analysis tools specially the indicator called (ratio of William index), and test the ability of technical analysis tools in building a portfolio of shares efficient in comparison with the market portfolio. These one technical tools were used for building one portfolios in 21 companies on specific preview conditions and choose 10 companies for the period from (March 2015) to (June 2017). Applied results of the research showed that Portfolio yield for companies selected according to the ratio of William index indicator (0.0406) that

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Publication Date
Wed Jul 30 2025
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Comprehensive Molecular Profiling of the 3′UTR Region of the CEBPA Gene in Iraqi Patients with Acute Myeloid Leukemia Reveals Novel Regulatory Variants
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Background: Acute myeloid leukemia (AML) is a genetically heterogeneous leukemia characterized by abnormal myeloid blast accumulation, disrupting normal hematopoiesis and leading to rapid progression. Objective: To investigate SNPs within the 3’UTR of the CCAAT/enhancer-binding protein alpha (CEBPA) gene and its association with AML in Iraqi patients. Methods: The study was carried out on 120 AML patients classified into newly diagnosed, induction chemotherapy, and consolidation chemotherapy stages (40 each), and 40 individuals as a control group. Genomic DNA was extracted from AML patients and controls, followed by PCR amplification and Sanger sequencing of the 3’UTR region of the CEBPA gene. The AML patients were characterized

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Publication Date
Fri Mar 13 2026
Journal Name
Al-fatih Journal
The impact of the use of some herbal sedative level of achievement in the development of air pistolEmpirical researchOn a sample of players Faculty of Physical Education for Girls
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تعد الرماية واحدة من الألعاب التي يقاس مستوى الانجاز فيها بالأرقام إذ ارتفعت الأرقام المسجلة بالنسبة لسلاح المسدس الهوائي حتى وصلت عند بعض الأبطال العالميين إلى الانجاز النهائي ، وقد لجأ المدربون إلى مختلف الطرق التدريبية, وان ضعف الثبات والتركيز هما اللذان يقودان إلى هبوط مستوى الانجاز في الرماية ، ولتحقيق التركيز والثبات المطلوبين أثناء الرمي يجب التدريب على مطاولة حمل السلاح التي تعد من أصعب تدريبات الر

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Publication Date
Fri Sep 29 2023
Journal Name
Cumhuriyet Dental Journal
Root Resorption in the Permanent Teeth. A Review
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The loss of dental hard tissue as a result of odontoclastic activity is known as root resorption. It is unwanted and pathological in permanent teeth. Root resorption may happen within the root canal called internal root resorption or on the outer surface of the root called external root resorption. Regardless of where it occurs, root resorption is irreparable, can cause pain for the patient, necessitates treatment, and in some circumstances, resulting in the early loss of the affected tooth. It might be challenging to precisely diagnose and treat root resorption. There is limited information within literatures on root resorption therefore this review aims to understand the radiological and clinical characteristics of r

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Publication Date
Wed Sep 15 2021
Journal Name
Al-adab Journal
The Iraqi countryside in a novel (Exceeded border)
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The novel was generally distinguished from other literary arts in its connection with the living reality as an imaginative practice that relies on political, economic, social, intellectual and cultural references and as a crucial tool in reading cultural references and dive deep into reality. As every novelist has a vision to embody this reality. As every novelist has a vision to embody this reality. The novel of ("Exceeded border by Hammed Al-Kafa’i) is a considered a fertile field for presenting social issues in their apparent structure and revealing the cultural patterns behind them which lies in its deep structure. The novel here moves its characters in its imaginary world in a way that it becomes more capable of adaptation and crysta

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Publication Date
Wed Feb 01 2023
Journal Name
Heat Transfer
A tubular solar still integrated with a heat pipe
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Abstract<p>The aim of this work is to explore the thermal performance of a tracked tubular solar still (TSS) with a parabolic trough concentrator in Baghdad (33.27° N, 44.37° E) in September 2022. The present tubular still is distinguished by its hexagonal glass cover. The effect of integrating the TSS with a heat pipe, the still tilt angle (10°, 15°), and the depth of saline water inside the still partitions on the productivity of freshwater are investigated. The results showed that using heat pipe enhances the freshwater productivity by 25%–40% and the efficiency by 25%. For the still integrated with heat pipe, as the water depth is increased from 5.5 to 6.5 cm the productivity of freshwater is incre</p> ... Show More
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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
Different garlic forms: (lobster, mashed, crushed) and their effect on quality qualities And the molecular life of the fermented cucumber and flavor
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This study aimed to isolate and identifye the growth of microorganisms and
their effect on pickled cucumber and cabbage, the study also investigated the effect of
garlic (in the form of segments, chopped or crushed) on the mentioned pickled –food
features . Furthermore, a sense based comparison is made between vinegar-preserved
samples and vinegar-garlic preserved ones.
The following results have been obtained:
1- The isolation of staph. aureus alone from the samples and the study of its physical
and biochemical features.
2- The fresh garlic (segments, chopped and crushed) with concentration of 5%, 7.5%,
and 10% showed a damaging percentage of 100% to bacterial growth of staph. Aureus
after 24 hours of inc

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Publication Date
Fri Mar 13 2026
Journal Name
Sciences Journal Of Physical Education
Using two types of electronic questions by applying the Quiz Creator program in the method of guided discovery and its effect on learning and maintaining a motor chain on the throat
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Publication Date
Mon Nov 06 2023
Journal Name
Eneurologicalsci
Dandy-Walker syndrome associated with a giant occipital meningocele: A case report and a literature review
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HTH Ahmed Dheyaa Al-Obaidi,", Ali Tarik Abdulwahid', Mustafa Najah Al-Obaidi", Abeer Mundher Ali', eNeurologicalSci, 2023

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