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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
Sat Dec 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
Finding the best estimation of generalized for failure rates by using Simulation
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The statistical distributions study aimed to obtain on best descriptions  of variable sets phenomena, which each of them got one behavior of that distributions .  The estimation operations study for that distributions considered of important things which could n't canceled in variable behavior study, as result  this research came as trial for reaching to best method for information distribution estimation which is generalized linear failure rate distribution, throughout studying the theoretical sides by depending on statistical posteriori methods  like greatest ability, minimum squares method and Mixing method (suggested method).        

The research

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Publication Date
Sun Jul 04 2021
Journal Name
Journal Of Interdisciplinary Mathematics
Comparison the solutions for some kinds of differential equations using iterative methods
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This manuscript presents several applications for solving special kinds of ordinary and partial differential equations using iteration methods such as Adomian decomposition method (ADM), Variation iterative method (VIM) and Taylor series method. These methods can be applied as well as to solve nonperturbed problems and 3rd order parabolic PDEs with variable coefficient. Moreover, we compare the results using ADM, VIM and Taylor series method. These methods are a commination of the two initial conditions.

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Publication Date
Mon Aug 06 2018
Journal Name
Indian Journal Of Applied Research
STATISTICAL METHOD FOR SOLVING TRANSPORTATION PROBLEMS OF USING THE PROGRAMMING LANGUAGE MATLAB
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Original Research Paper Mathematics 1-Introduction : In the light of the progress and rapid development of the applications of research in applications fields, the need to rely on scientific tools and cleaner for data processing has become a prominent role in the resolution of decisions in industrial and service institutions according to the real need of these methods to make them scientific methods to solve the problem Making decisions for the purpose of making the departments succeed in performing their planning and executive tasks. Therefore, we found it necessary to know the transport model in general and to use statistical methods to reach the optimal solution with the lowest possible costs in particular. And you know The Transportatio

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Publication Date
Mon Oct 01 2018
Journal Name
Iraqi Journal Of Physics
Using the plastic wastes in fabrication of composite materials for different applications
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This study suggests using the recycled plastic waste to prepare the polymer matrix composite (PMCs) to use in different applications. Composite materials were prepared by mixing the polyester resin (UP) with plastic waste, two types of plastic waste were used in this work included polyethylene-terephthalate (PET) and Polyvinyl chloride (PVC) with varies weight fractions (0, 5, 10, 15, 20 and 25 %) added as a filler in flakes form. Charpy impact test was performed on the prepared samples to calculate the values of impact strength (I.S). Flexural and hardness tests were carried out to calculate the values of flexural strength and hardness. Acoustic insulation and optical microscope tests were carried out. In general, it is found that UP/PV

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Publication Date
Thu Apr 01 2010
Journal Name
Journal Of Educational And Psychological Researches
The Effect of Using Computer in program BasedStudying for Student in Jordan
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This study aimed at investigating the effect of using computer in
Efficiency of Training Programme of Science Teachers in Ajloun District in
Jordan.
1- What is the effect of using computer in program for the two groups
2- ( the experimental and control group ) .
3- Are there any statistics different in the effect of using computer
program for the two groups ?
4- Are there any statistics (comparison ) or different of the effect of the
effect of using computer program refer to the sex (male or female )?
The community of the study consisted of all the science student in
educational directorate of Ajloun district for the academic year 2009 –
2010, they are (120) ( male and female) . The sample of the study<

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Publication Date
Wed Oct 01 2025
Journal Name
Chinese Journal Of Analytical Chemistry
Synthesis, characterization, antioxidant and bioactivity assessment, and thermodynamic analysis of metal ion complexes using a novel azo dye
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Publication Date
Wed Oct 01 2014
Journal Name
Engineering And Technology Journal
Investigating Forward kinematic Analysis of a 5-axes Robotic Manipulator using Denavit-Hartenberg Method and Artificial Neural Network
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Publication Date
Mon Feb 01 2016
Journal Name
Journal Of Engineering
Removal of Fluoride Ions from Wastewater Using Green and Blue-green Algae Biomass in a Fluidized Bed System
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The removal of fluoride ions from aqueous solution onto algal biomass as biosorbent in batch and continuous fluidized bed systems was studied. Batch system was used to study the effects of process parameters such as, pH (2-3.5), influent fluoride ions concentration (10- 50 mg/l), algal biomass dose (0–1.5 g/ 200 ml solution), to determine the best operating conditions. These conditions were pH=2.5, influent fluoride ions concentration= 10 mg/l, and algal biomass dose=3.5 mg/l. While, in continuous fluidized bed system, different operating conditions were used; flow rate (0.667- 0.800 l/min), bed depth (8-15 cm) corresponded to bed weight of (80- 150 g). The results show that the breakthrough time increases with the inc

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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
Sun Jan 01 2023
Journal Name
The Egyptian Journal Of Hospital Medicine
Training of Skilled Force with The Different Medical Ball and Their Effect on Developing Some Special Physical Abilities and the Accuracy of Long Shooting Performance in Handball
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