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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 Jan 01 2024
Journal Name
Journal Of Applied Pharmaceutical Science
The role of angiotensin converting enzyme (insertion)/(deletion) and angiotensin II type 1 receptor (A1166C) gene polymorphisms in antiproteinuric effect of ACE inhibitors in type 2 diabetic Iraqi patients
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The angiotensin converting enzyme (ACE) I\D gene polymorphism influences the blood ACE enzyme activity. Renoprotective effect of ACE inhibitors (ACEIs) varies among patients due to genetic variation, particularly in Renin-Angiotensin-Aldosterone System genes. This study investigates the genetic variations of ACE I\D and AGT1RA1166C gene polymorphisms in the antiproteinuric effect of ACEI therapy in type 2 diabetes mellitus (T2DM) patients. This is a cross-sectional study that included 76 T2DM patients who are ACEI users, divided into two groups: T2DM without diabetic kidney disease (DKD) included 31 patients, and T2DM with DKD included 45 patients. Urine samples were taken for measurement of urine albumin and creatinine, then calcul

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Publication Date
Sun Aug 05 2018
Journal Name
Journal Of Entomology And Zoology Studies
Some biochemical traits in broiler chicken as affected by insulin-like growth factor-1 (IGF-1) gene polymorphisms
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This study was conducted during the period 1/9/2014 – 1/2/2015 and aimed to identify the polymorphisms of IGF-1 gene in broiler chickens and their effects on some biochemical traits. A total of 300 one-day-old broiler chicks (Cobb500, n=150; Hubbard F-15, n=150) were evaluated in this study. Blood samples were individually collected from all birds for DNA extraction. PCR-RFLP method being used for determination the genotypes of IGF-1 gene which then correlated with biochemical traits studied. Cobb500 broilers with TT genotype had significantly (p˂0.05) higher serum triglycerides values than those of TC and CC genotypes. Low density lipoprotein (LDL) were significantly (p˂0.05) higher in Hubbard F-15 broilers with TT genotype than those

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Publication Date
Thu Dec 01 2022
Journal Name
Environmental Nanotechnology Monitoring & Management
Green approach for the synthesis of graphene glass hybrid as a reactive barrier for remediation of groundwater contaminated with lead and tetracycline
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Publication Date
Thu Jan 10 2019
Journal Name
The Astrophysical Journal
A Deeply Buried Narrow-line Seyfert 1 Nucleus Uncovered in Scattered Light
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Publication Date
Thu Aug 18 2022
Journal Name
Journal Of Interdisciplinary Mathematics
The dynamics of Coronavirus pandemic disease model in the existence of a curfew strategy
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Publication Date
Fri Jan 01 2021
Journal Name
Review Of International Geographical Education
Evaluating the performance of project management using network diagrams methods: A case study in the Ramadi Municipality
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This study came for the reason that some project administrations still do not follow the appropriate scientific methods that enable them to perform their work in a manner that achieves the goals for which those projects arise, in addition to exceeding the planned times and costs, so this study aims to apply the methods of network diagrams in Planning, scheduling and monitoring the project of constructing an Alzeuot intersection bridge in the city of Ramadi, as the research sample, being one of the strategic projects that are being implemented in the city of Ramadi, as well as being one of the projects that faced during its implementation Several of problems, the project problem was studied according to scientific methods through the applica

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Publication Date
Fri Feb 08 2019
Journal Name
Journal Of The College Of Education For Women
The role of an active teacher in developing the curriculum by using educational techniqes a theoretical study
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Preparing teacher occupies the attention of many thinkers and philosophers since the age of
kaldinics ( people of mesoptam / 2342 pH ) to the Islamic age where moslems philosophers
focus their attention on thought and philosophy where the philosophy of that teaching
depends on : teacher , student and family begin .
So , the issue of preparing and training teacher occupies the attention of education scientists
depending on his vital and important role in implementing of teaching policies in philosophies
and Islamic educational thought , therefore , the preparing and development of the teacher
regards as one of the basics of teaching development because of its importance in
development of teaching performance and th

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Publication Date
Wed Apr 01 2015
Journal Name
Al–bahith Al–a'alami
The Educational Role of Children's Programs in Libyan TV An Analytical -Field Study of "Flowers of Life" Program
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Television contributes children the acquisition of knowledge, moral and social values through programs that are offered to them and the extent of the focus on the effective aspects of life in the age of the target stage. The subject of this research aims to know the children programs in Libya television through a comprehensive analytical study of the program entitled “zihur al-hayat” within the broadcast season from April 1, 2004 to June 30, 2004. It also focuses on trying to identify the Libyan television policy in broadcast educational content through the children's programs in the prevailing political and social conditions during the period of study as well as knowing the opinions of the children's sample under study in Al-Baidhaa

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Publication Date
Tue Feb 27 2024
Journal Name
Tem Journal
Supervised Classification Accuracy Assessment Using Remote Sensing and Geographic Information System
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Assessing the accuracy of classification algorithms is paramount as it provides insights into reliability and effectiveness in solving real-world problems. Accuracy examination is essential in any remote sensing-based classification practice, given that classification maps consistently include misclassified pixels and classification misconceptions. In this study, two imaginary satellites for Duhok province, Iraq, were captured at regular intervals, and the photos were analyzed using spatial analysis tools to provide supervised classifications. Some processes were conducted to enhance the categorization, like smoothing. The classification results indicate that Duhok province is divided into four classes: vegetation cover, buildings,

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Publication Date
Sat Jun 01 2024
Journal Name
International Journal Of Advanced And Applied Sciences
High-accuracy models for iris recognition with merging features
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Due to advancements in computer science and technology, impersonation has become more common. Today, biometrics technology is widely used in various aspects of people's lives. Iris recognition, known for its high accuracy and speed, is a significant and challenging field of study. As a result, iris recognition technology and biometric systems are utilized for security in numerous applications, including human-computer interaction and surveillance systems. It is crucial to develop advanced models to combat impersonation crimes. This study proposes sophisticated artificial intelligence models with high accuracy and speed to eliminate these crimes. The models use linear discriminant analysis (LDA) for feature extraction and mutual info

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