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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
Tue Jun 15 2021
Journal Name
Al-academy
The concept of freedom in the texts of Yashar Kamal play "The play (The Plate) as a model": عامر صباح نوري المرزوك
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This research is concerned with studying (the concept of freedom in the texts of Yaşar Kamal the play), as the Turkish playwright (Kamal Yasar) is one of the contemporary playwrights who have been interested in and criticize society, and perhaps the concept of freedom in his texts took a different form, through his ability to renew and present his attempts to create A theatrical form different from his earlier writers in dealing with the life of the peasants and the oppression that went through them, as the researcher identified the problem of his research with the following question: What is the concept of freedom in the texts of Yashar Kamal? The research aims to define the concept of freedom in the texts of Yashar Kamal of the play,

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Publication Date
Mon Nov 02 2020
Journal Name
International Journal Of Pharmaceutical Research
Serum Afamin As A Novel Biomarker for Non-Alcoholic Fatty Liver Disease as A Complication of Hypothyroidism in Iraqi Patients.
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Publication Date
Mon Dec 31 2018
Journal Name
Ibn Al-haitham Jour. For Pure & Appl. Sci
Comparative Study of Thymidine Kinase -1 and Total Antioxidant Capacity in Iraqi Children with Platelet Count Disorder
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This study aimed to find relationship between thymidine kinase-1 (TK-1) as tumor marker and total antioxidant capacity (TAC) in Iraqi children patients with thrombocytopenia and with thrombocytosis. The present study conducted 60 children patients (30 patients with idiopathic thrombocytopenia purpura (ITP) and 30 patients with thrombocytosis caused by leukemia) attending the Children Fever Hospital in the Medical City / Baghdad, and 30 healthy children as a control group. All study groups were with range ages (1-15) years, and they were diagnosed by assay of platelet count, Prothrombin Time (PT), and partial Thromboplastin Time (PTT). The results shown elevation in plasma TK-1 and TAC values in children patients with thrombocytopenia and w

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Publication Date
Fri Aug 12 2016
Journal Name
Iraqi Dental Journal
Pacifier Sucking Habit and its Relation to Oral Health of Children Aged 1-5 Years (comparative study)
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Publication Date
Wed Jun 29 2022
Journal Name
College Of Islamic Sciences
AYĀT AL-HUJJAH FĪ SŪRAT AL-ANĀM RIWĀIAH WA DERĀIAH ( a model in three verses from Surat Al-An’am 108-110)
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The current research discusses the jurisprudence of the argumentative meaning in the Qur’an, and it is one of the general methods of responses in the Qur’an, as well as the argumentative approach to the recitations of the readers and directing their meanings. I have chosen a model for three verses from Surat Al-An’am, in which there are seven frequent recitations and seven odd ones, on a topic related to theology and faith; It forms the centerpiece of the argument verses in Surat Al-An'am; It contains the jurisprudence of dealing with infidels and dissenters, turning away and forbidding insulting what they claim besides God in the event of corruption, and God Almighty’s decree and wisdom in the occurrence of unbeli

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Publication Date
Tue Jun 20 2023
Journal Name
Bulletin Of The Iraq Natural History Museum
A COMPARATIVE-MORPHOLOGICAL STUDY OF SKULLS IN TWO SPECIES OF CARNIVOROUS AND HERBIVOROUS MAMMALS
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The skull is one of the largest bones in the body. It is classified into flat bones that maintain the important organic structures; which are the brain, eyes, and tongue. The skull is a strong support for preserving these organs but they are various according to the type of animals and the environments in which they live and the nature of their nutrition. There are many differences among living organisms in terms of the bones in the skull, their difference or disappearance and their length in the shape of the head. The samples were taken from the scientific storage in the Iraq Natural History Research Center and Museum; Cape hare Lepus capensis (Linnaeus, 1758) and Red fox Vulpes vulpes (Linnaeus, 1758) and the study was conducted o

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Publication Date
Tue Jun 20 2023
Journal Name
Bulletin Of The Iraq Natural History Museum
A COMPARATIVE-MORPHOLOGICAL STUDY OF SKULLS IN TWO SPECIES OF CARNIVOROUS AND HERBIVOROUS MAMMALS
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The skull is one of the largest bones in the body. It is classified into flat bones that maintain the important organic structures; which are the brain, eyes, and tongue. The skull is a strong support for preserving these organs but they are various according to the type of animals and the environments in which they live and the nature of their nutrition. There are many differences among living organisms in terms of the bones in the skull, their difference or disappearance and their length in the shape of the head. The samples were taken from the scientific storage in the Iraq Natural History Research Center and Museum; Cape hare Lepus capensis (Linnaeus, 1758) and Red fox Vulpes vulpes (Linnaeus, 1758) and the study was conducted o

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Publication Date
Sun Feb 18 2024
Journal Name
Fitness, Performance And Health Journal
A Comparative Study of Some Types of Muscular Strength Among Middle-Distance Runner Athletes
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The research aims to conduct a comparative study between the events (800) m and (1500) m track in the types of muscular strength and to identify the differences between them among Iraqi sports club players. The sample represented the players participating in the Iraqi Athletics Championship for the period between (02/11/2023) and (04 /11/2023), and their number was (16) players (8) for each event, as the selection was made intentionally.  The researchers used the descriptive approach to achieve the goal of the research and used the statistical package (SPSS) to process the data statistically. According to the results collected, it was found that there was superiority among the intermediate track players (800) m in explosive power and the s

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Publication Date
Mon Jan 01 2024
Journal Name
Aip Conference Proceedings
A multivariate Bayesian model using Gibbs sampler with real data application
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In many scientific fields, Bayesian models are commonly used in recent research. This research presents a new Bayesian model for estimating parameters and forecasting using the Gibbs sampler algorithm. Posterior distributions are generated using the inverse gamma distribution and the multivariate normal distribution as prior distributions. The new method was used to investigate and summaries Bayesian statistics' posterior distribution. The theory and derivation of the posterior distribution are explained in detail in this paper. The proposed approach is applied to three simulation datasets of 100, 300, and 500 sample sizes. Also, the procedure was extended to the real dataset called the rock intensity dataset. The actual dataset is collecte

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Publication Date
Tue Jan 01 2019
Journal Name
Therapeutic Advances In Drug Safety
Deferasirox in thalassemia: a comparative study between an innovator drug and its copy among a sample of Iraqi patients
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Background:

The health care industry is witnessing an increasing trend in the use of generic medicines because of their presumed low cost compared with innovator medicines. The aim of this study was to determine and compare the performance of the copy drug Osveral®and its innovator drug deferasirox (Exjade®).

Methods:

A prospective observational study including 223 patients receiving the branded medicine Exjade®and 101 patients receiving the copy Osveral®was carried out. Data were assessed for a 1-year period and included clinical symptoms, serum ferrit

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