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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
Fri Jan 01 2016
Journal Name
Results In Physics
Optimization of dye extraction from Cordyline fruticosa via response surface methodology to produce a natural sensitizer for dye-sensitized solar cells
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Publication Date
Sun Mar 04 2012
Journal Name
Baghdad Science Journal
Adsorption Study for Trifluralin on Iraqi ? –Alumina
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Equilibrium adsorption isotherm for the removal of trifluralin from aqueous solutions using ? –alumina clay has been studied. The result shows that the isotherms were S3 according Giels classification. The effects of various experimental parameters such as contact time, adsorbent dosage, effect of pH and temperature of trifluralin on the adsorption capacities have been investigated. The adsorption isotherms were obtained by obeying freundlich adsorption isotherm with (R2 = 0.91249-0.8149). The thermodynamic parameters have been calculated by using the adsorption process at five different temperature, the values of ?H, ?G and ?S were (_1.0625) kj. mol-1, (7.628 - 7.831) kj.mol-1 and (_2.7966 - _2.9162) kg.

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Publication Date
Sun Dec 01 2013
Journal Name
Political Sciences Journal
Political behavior for generations (Iraq's case study)
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The topic area of that’s research dealing with values which adopted by Iraqi people since 1980, many changes and variables which make many situations and skills which the life is suitable in war and conflicts times. That’s values like traditional and ordering, traditionalism mean the conservation about values s and tradition which society adopted its. The Iraqi society suffering from many changes since 1980-2003, the consequently of that’s changes make Iraqi citizen more interested about luxury needs like clothes, while decreasing the interested about liberty of thought, beauty, show evidence of identity, and openness of mind. The processing of values changes associated with political behavior of Iraqi people which lead to weaken o

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Publication Date
Wed Dec 01 2010
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Statistical study for Indian quasi-stable population
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During more than (50) years past, India has achieved considerable social and economic progress. It is also generally assumed that the future progress will be even more rapid and that India will be an important player in the global market. India has only (2.5) percent of global land whereas it has to provide home for one-sixth of world's population .On examining the past trends of India's population ,it may be observed that during the latter half of the twentieth century ,about (650) million populations were added to the country ,thus living in a country with a high population density and high growth rate , India in need a transition from high fertility high mortality to a low fertility low mortality and towards stable population situatio

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Publication Date
Fri Feb 08 2019
Journal Name
Iraqi Journal Of Laser
Photodynamic Therapy for Leiomyosarcoma: In vitro study
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Leiomyosarcoma (smooth muscle tumor) is a rare type of a malignant neoplasm of smooth
muscle. It is a resistant cancer, generally not very responsive to chemotherapy, radiationand surgery.The
aim of this study was to evaluate photodynamic therapy (PDT) as a possible basis for treatment using
(650 nm)diode laser with methyleneblue (MB) as a photosensitizer on leiomyosarcoma (LMS)cell line
(L20B) in vitro. The cytotoxic effects of 650nm diode laser 0.052 W/cm2 (power density) at different
exposure time (10, 20, and 30 min) with methylene blue at different concentrations (0.01% ,0.1 % ,1%)
was investigated on LMS cell line (L20 B). The cytotoxic effect of laser was increased with increasing
irradiation time for a certai

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Publication Date
Tue Jan 01 2019
Journal Name
Indian Journal Of Public Health Research & Development
Anticardiolipin Antibodies in Comparison to B-HCG Titer and Serum Progesterone as Indicator for Ectopic Pregnancies
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Publication Date
Fri Dec 15 2023
Journal Name
Iraqi Journal Of Laser
Silver Nanoflowers as an Interfacial Liquid-State Surface Enhanced Raman Spectroscopy (SERS) Sensor for Water Pollution
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Water pollution has created a critical threat to the environment.‎‎ A lot of research has been done ‎recently to use surface-enhanced Raman spectroscopy (SERS) to detect multiple pollutants in water. This study aims to use Ag colloid nanoflowers as liquid SERS enhancer. Tri sodium phosphate (Na3PO4) was investigated as a pollutant using liquid SERS ‎based on colloidal Ag ‎nanoflowers. The chemical method was used to synthesize nanoflowers from silver ‎ions. Atomic Force Microscope (AFM), Scanning Electron Microscope (SEM), and X-ray diffractometer (XRD) were employed to characterize the silver nanoflowers. This ‎nanoflowers SERS action in detecting Na3PO4 was reported and analyzed

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Publication Date
Wed Mar 15 2023
Journal Name
Journal Of Baghdad College Of Dentistry
Complete Blood Count and saliva parameters as an indicator for infected patients with coronavirus covid-19
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Background: Coronavirus, which causes respiratory illness, has been a public health issue in recent decades. Because the clinical symptoms of infection are not always specific, it is difficult to expose all suspects to qualitative testing in order to confirm or rule out infection as a test. Methods: According to the scientific studies and investigations, seventy-three results of scientific articles and research  were obtained using PubMed, Medline, Research gate and Google Scholar. The research keywords used were COVID-19, coronavirus, blood parameters, and saliva. Results: This review provides a report on the changes in the blood and saliva tests of those who are infected with the COVID-19.COVID-19 is a systemic infection that has

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Publication Date
Tue Apr 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
Evaluation Age and Gender for General Census of the population in Iraq by using nonparametric Bayesian Kernel Estimators
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The process of evaluating data (age and the gender structure) is one of the important factors that help any country to draw plans and programs for the future. Discussed the errors in population data for the census of Iraqi population of 1997. targeted correct and revised to serve the purposes of planning. which will be smoothing the population databy using nonparametric regression estimator (Nadaraya-Watson estimator) This estimator depends on bandwidth (h) which can be calculate it by two ways of using Bayesian method, the first when observations distribution is Lognormal Kernel and the second is when observations distribution is Normal Kernel

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
The relationship between the central government and local administrations in the federal system: Experience the Iraqi model
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   Increasingly, public organizations in the federal state are required to work together, as well as to work with others to achieve their objectives. In Iraq there are two levels of organizations, including federal and local, and these organizations have been forced to work for many years in an environment in which the responsibility for service delivery is shared between policy makers and service providers, and between local governments and the federal government. It is sometimes difficult to manage the relationship between these organizations (federal and local) and do not always provide the best possible outcome of this relationship. This paper reviews how to manage the relationship between local administrations and

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