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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 Oct 28 2023
Journal Name
Baghdad Science Journal
Experimental Investigation of the Mechanical and Structural Properties of a Functionally Graded Material by Adding Alumina Nanoparticles Using A Centrifugal Technique
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In this work, functionally graded materials were synthesized by centrifugal technique at different
volume fractions 0.5, 1, 1.5, and 2% Vf with a rotation speed of 1200 rpm and a constant rotation time, T
= 6 min . The mechanical properties were characterized to study the graded and non-graded nanocomposites
and the pure epoxy material. The mechanical tests showed that graded and non-graded added alumina
(Al2O3) nanoparticles enhanced the effect more than pure epoxy. The maximum difference in impact strength
occurred at (FGM), which was loaded from the rich side of the nano-alumina where the maximum value was
at 1% Vf by 133.33% of the sample epoxy side. The flexural strength and Young modulus of the fu

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Publication Date
Mon Oct 01 2018
Journal Name
World Journal Of Pharmacy And Pharmaceutical Sciences
THE ANTIBACTERIAL EFFECT OF FLAXSEED EXTRACT ON SELECTIVE ORAL PATHOGENS - COMPARATIVE IN VITRO STUDY
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Flaxseed from the flax plant (Linum usitatissimum), which has been cultivated for domestic use since prehistoric times. This study aims to investigate presence of antibacterial effect of flaxseed extract against selected oral pathogen in-vitro.

Publication Date
Fri May 25 2018
Journal Name
Open Public Health Journal
Comparative Study on the Clinicopathological Profiles of Breast Cancer Among Iraqi and British Patients
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Background: Breast cancer is the most common cancer in Iraq and the United Kingdom. While the disease is frequently diagnosed among middleaged Iraqi women at advanced stages accounting for the second cause of cancer-related deaths, breast cancer often affects elderly British women yielding the highest survival of all registered malignancies in the UK. Objective: To compare the clinical and pathological profiles of breast cancer among Iraqi and British women; correlating age at diagnosis with the tumor characteristics, receptor-defined biomarkers and phenotype patterns. Methods: This comparative retrospective study included the clinical and pathological characteristics of (1,940) consecutive female patients who were diagnosed with invasive b

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Publication Date
Sun Jan 01 2017
Journal Name
Iraq Journal Of Agricultural Research
THE COMPARATIVE STUDY OF THE TOTAL COSTS AND NET REVENUE OF DIFFERENT TILLAGE SYSTEMS USING TWO TYPES OF SEEDLINGS IN THE PRODUCTION OF BARLEY GREEN VARIETY SAMEER IN THE GYPSUM SOILS
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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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Publication Date
Thu Jun 30 2022
Journal Name
Iraqi Journal Of Laser
PDF Towards C+L Band Three-Mode (De)Multiplexer Using Subwavelength Grating (SWG) Technology
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Abstract: Recently, there is increasing interest in using mode-division multipelexing (MDM) technique  to enhace  data rate transmission over multimode fibers.  In this technique, each fiber mode is treated as a separate optical carrier to transfer its own data.  This paper presents a broadband, compact, and low loss three-mode (de)multiplexer designed for C+L band using subwavelength grating (SWG) technology and built-in silicon-on-insulator SOI platform. SWG offers refractive index engineering for wider operating bandwidth and compact devices compared to conventional ones. The designed (de)multiplex deals with three modes (TE0, TE1, and TE2) and has a loss > -1 dB and crosstalk < −15 dB, and its operation c

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Publication Date
Sat Dec 31 2022
Journal Name
International Journal Of Intelligent Engineering And Systems
Using Three-Dimensional Logistic Equations and Glowworm Swarm Optimization Algorithm to Generate S-Box
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Publication Date
Mon Jan 01 2018
Journal Name
Ibn Al-haitham J. For Pure & Appl. Sci
Comparative Anatomical Study between Typhadomengensis and Phragmites communis
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Both of the species Typha domengensis and Phragmites communis among the most important plant endemic in flora of Iraq from monocotyledon. Due to the similarity of the two species with each other in many morphological characteristics such as the environment where they live and the form of leaves and type of leaf venation and type of stomata….ets, also both of species belong to monocots plant therefore this research work was conducted find anatomical differences that have the same as taxonomic value to help distinguishing between both species under study. Through this research, we found great importance to the anatomical characteristics which we reached by studying the roots, stems and leaves sections f

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Publication Date
Thu Mar 30 2023
Journal Name
College Of Islamic Sciences
The effect of readings on the multiplicity of explanatory significance of a single Qur’anic word, a study through the interpretation of Ibn Attia al-Andalusi
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The study aimed to clarify the meanings learned and inferred from reading books، letters and messages in Surat Al-Qur’an. The inductive method، the analytical method، and the deductive method، One of the most prominent results of the research: that the multiplicity of Qur’anic readings produces a variety and expansion in the meaning that has a clear impact on the interpretation by clarifying the meaning of the verse.

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Publication Date
Sun Mar 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
Evolution and set up the maps for solar radiation of Iraq using Data observation and Angstrom model during monthly July2017
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Abstract<p>The development that solar energy will have in the next years needs a reliable estimation of available solar energy resources. Several empirical models have been developed to calculate global solar radiation using various parameters such as extraterrestrial radiation, sunshine hours, albedo, maximum temperature, mean temperature, soil temperature, relative humidity, cloudiness, evaporation, total perceptible water, number of rainy days, and altitude and latitude. In present work i) First part has been calculated solar radiation from the daily values of the hours of sun duration using Angstrom model over the Iraq for at July 2017. The second part has been mapping the distribution of so</p> ... Show More
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