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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 Nov 06 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
Effect of hunting cooperation and fear in a food chain model with intraspecific competition
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Taking into account the significance of food chains in the environment, it demonstrates the interdependence of all living things and has economic implications for people. Hunting cooperation, fear, and intraspecific competition are all included in a food chain model that has been developed and researched. The study tries to comprehend how these elements affect the behavior of species along the food chain. We first examined the suggested model's solution properties before calculating every potential equilibrium point and examining the stability and bifurcation nearby. We have identified the factors that guarantee the global stability of the positive equilibrium point using the geometric approach. Additionally, the circumstances that would gu

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Publication Date
Thu Dec 20 2007
Journal Name
Journal Of Planner And Development
To contribute in handling the housing crisis in the city of BaghdadA study for the decision of the Mayoralty of Baghdad to allow adding a third floor for the residential units
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We need to know the basic facts concerning planning top and bottom limits including any critical levels or the threshold over which the cost would be much higher for land development. Therefore this paper concerned with Baghdad Municipality decision No.2/1004 dated 7/12/2004. The reason behind this decision is the hope to face up at least in the severe housing crisis in the city of Baghdad. This paper attempts to know the attitude of the local community in the general through a field study of people living near such dwelling where third floors are added of. This might indicate any positive or negative effects whether on short or long-term including its effect on the theoretical side including the population growth of Baghdad, the

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Publication Date
Sun Dec 10 2023
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Detection of Multiple Sclerosis Lesions in Supra- and Infra-Tentorial Anatomical Regions by Double Inversion Recovery, Flair, and T2 MRI Sequences: A Comparative Study in Iraqi Patients
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Background: In young adults, multiple sclerosis is a prevalent chronic inflammatory demyelinating condition. It is characterized by white matter affection, but many individuals also have significant gray matter involvement. A double-inversion recovery pulse (DIR) pattern was recently proposed to improve the visibility of multiple sclerosis lesions. Objective: To find out how well a DIR sequence, FLAIR, and T2-weighted pulse sequences can find MS lesions in the supratentorial and infratentorial regions. Methods: A total of 37 patients with established diagnoses of multiple sclerosis were included in this cross-sectional study. Brain MRI was done using double inversion recovery, T2, and FLAIR sequences. The number of lesions was count

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Publication Date
Fri May 05 2023
Journal Name
International Journal Of Professional Business Review
The Effect of Emotional Intelligence on Manager Performance: a Field Study in the General Authority for Irrigation and Reclamation Projects in Baghdad
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Purpose: the purpose of this study is to investigate how managers working for the General Authority for Irrigation and Reclamation Projects react to the impact of Emotional Intelligence (EI) on their performance.   Theoretical framework: The current study includes an intellectual framework on two variables, namely EI and Manager Performance (MP), because it is essential to investigate the relationship between these two variables and the impact of EI on MP.   Design/methodology/approach: The research problem is that a manager's capacity to make wise decisions about their work or interactions with subordinates is diminished when they have inadequate EI. The questionnaire is used as a tool for gathering data for the study, and the st

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Publication Date
Thu Jan 09 2020
Journal Name
Plant Archives
Molecular Study of Two Fungi Millerozyma Farinosa and Candida Orthopsilosis by PCR Using Its Gene and Phylogenetic Structuring Tree Isolated from Diabetic Patient in Baghdad
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Diabetic mellitus is one of the main risk factors of fungal infections because poor glycemic control is associated with a high level of glucose in blood and saliva which could be treated as nutrient to fungi. This study aimed to isolate and identification of pathogenic fungi from diabetic patient. 140 samples were taken from different places of human body from the national center of diabetic patients that related to Mustansiriyah University / college of medicine and Al-yarmuk Hospital in Baghdad. 84 sample (60%) tested positive to fungi and 56 sample (40%) tested negative to fungi. The most frequented fungi isolated have been chosen for molecular identification by PCR (Millerozyma farinosa and Candida orthopsilosis) using specific pri

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Publication Date
Sun Jan 01 2023
Journal Name
Studies In Systems, Decision And Control
Gap Analysis by Readiness Review Including Online Learning During COVID-19 Pandemic Period for Engineering Programs at the College of Engineering—University of Baghdad
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Publication Date
Wed Oct 26 2022
Journal Name
Petroleum Science And Technology
Building 3D geological model using non-uniform gridding for Mishrif reservoir in Garraf oilfield
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Publication Date
Wed Apr 01 2020
Journal Name
Technology Reports Of Kansai University
Complex of Lascoux in the General Case of Three Rows
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Publication Date
Sun Dec 01 2024
Journal Name
Baghdad Science Journal
Synthesis, Characterization and Antioxidant Study of Some Metal Ion Complexes with Azo 1-(2,4,6-trihydroxy-3-((3-hydroxyphenyl) diazenyl) phenyl) Ethan-1-one.
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اثناء تفاعل الديزنة تكونت صبغة أزو جديدة عن طريق تفاعل 3-امينوفينول مع 2,4,6-ثلاثي هيدروكسي اسيتوفينون . ثم تم تفاعل هذا الليكاند مع بعض ايونات العناصر الكروم والحديد الروديوم والروثينيوم بتكفؤهم الثلاثي والكوبلت الثنائي والموليبدينوم سداسي التكافؤ مكونة معقدات فلزية مختلفة بأشكال هندسية متعددة. تم ملاحظة تناسق مجموعة الازو مع ايونات العناصر من خلال ملاحظة ظهور حزم امتصاص الفلز مع النتروجين والاوكسجين ب

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Publication Date
Thu Feb 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Measure the Impact of global financial crisis on some indicators of the Saudi Arabia's economy using the Mendel-Fleming model for period (1997-2015)
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         The main objective of this study is to measure the Impact of global financial crisis on some indicators of the Saudi Arabia's economy using the Mendel-Fleming model, the importance of the study applied by focusing on the theme of general equilibrium in the face of fluctuations in the global economy. Study used a descriptive approach and the methodology of econometrics to construct the model. Study used Eviews Program for data analysis. The Data was collected from the Saudi Arabian Monetary Agency, for the period (1997-2014).Stationery of the variables was checked by Augmented Dickey-Fuller (ADF) and Phillips Perron (PP) unit roots tests. And also the co-integration

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