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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
Sun Apr 03 2016
Journal Name
Journal Of The Faculty Of Medicine Baghdad
Nosocomial infections in a Surgical Floor of the General Ba’qubah Hospital; Iraq
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Background: Prevention against nosocomial infection is an important issue of health care field and considered a challenge of patients’ since it reflects its effect on their quality of life. This due to that it will lead in most cases to prolonged hospitalization and also more cost.Objective: To determine the prevalence of different types of nosocomial infection and to demonstrate the association of different risk factors (hospital environment, workers, visitors) with nosocomial infection.Patients: this study was carried out in eleven months at Ba’quba general Hospital; Iraq. A total of 81 clinical specimens (urine, pus from abscess , burn swab, nasal swab, ear swab and wound swab) taken from surgical patients,102 specimens from

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Publication Date
Tue Sep 30 2025
Journal Name
Medical Journal Of Babylon
Pompe Disease (A Rare Metabolic Disease) in Basrah, the South of Iraq
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Pompe disease is a progressive, multisystemic, debilitating, often fatal neuromuscular disease caused by a pathogenic variant in the acid α-glucosidase gene leading to GAA enzyme deficiency and lysosomal glycogen accumulation. Objectives: This study aimed to determine the prevalence of early onset Pompe disease in Basra, using the dried blood spot (DBS) as a screening tool, also to determine the spectrum of presentation. Materials and Methods: In a prospective study conducted in Basrah, Iraq, from October 2021 to September 2023, all infants with a family member diagnosed as a case of Pompe disease, hypotonia, or ventricular hypertrophy referred to the pediatric cardiology unit in Basra Cardiac Hospital were subjected to echocardiographic e

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Publication Date
Mon Jan 15 2018
Journal Name
International Journal Of Science And Research (ijsr)
Production a Digital Map with the Aid of Total Station and (GIS)
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Geographic information system (GIS) is utilized in a variety of tasks such as, resource management, urban planning, emergency planning in case of accident, and rapid response etc. The aim of this study is to produce a digital map with the aid of GIS and a survey data. A survey data is conducted with Total Station technique on sanitary planning positions. The campus of Baghdad University is chosen to test the execution and accuracy of the results for sewer manholes locations. During the field survey, Total Station (Nikon Nivo) is used to identify the 3-D coordinates for each location. Finally, Geographical Information System (GIS) are utilized to present the digital map of the network sewer pipe line to the end users. Although Geographic Inf

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Publication Date
Thu Oct 06 2022
Journal Name
2022 9th International Conference On Electrical Engineering, Computer Science And Informatics (eecsi)
On the Performance of a Composite Right Left Hand Electromagnetic Bandgap Structure
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This paper presents the design and analysis of composite right left hand (CRLH) electromagnetic bandgap (EBG) structure. The proposed unit cell is consistent of a dielectric substrate with dimensions of 5×5×1 mm 3 made of FR4-Epoxy with εr = 4.4 underneath of a conductive patch with dimensions of 4.4×4.4mm 2 . The unit cell is structured to perform a negative permittivity (ε) and negative permeability (µ) in different bands. The proposed unit cell is developed to 5G systems in the sub-6GHz bands. In this work, a complete analysis of the unit cell in terms of Sparameters, constitutive parameters and refraction index are evaluated using HFSS simulation package based on Finite Element Method (FEM).

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Publication Date
Sat Jun 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
The nature of financial system Is it an necessity or A selection?
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   The Financial systems can be classified into two types. The first is the market–oriented, which is applied in United States and United Kingdom. While the second is bank-oriented as in Japan and Germany.

   This study tries to explain the reasons which make some countries adopt the first one instead of the second, and the contrary. So the study consists of three sections. The first deals with the concept of financial system and it are functions. The second displays the indicators which are used to classify the financial systems, while the third one is devoted to the factors that determine the type of financial system .These sections followed by some conclusions.

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Publication Date
Sat Jun 30 2012
Journal Name
Al-kindy College Medical Journal
Angiolymphoid Hyperplasia with Eosinophilia : a Case Report and Review of the Literature
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A case of angiolymphoid hyperplasia with eosinophilia (ALH) is reported in a 42-year-old woman who developed multiple nodules behind the ear. Angiolymphoid hyperplasia with eosinophilia usually occurs on the head and neck of young adults and is more common in women than in men. Characteristic histologic features of ALH present in this case included proliferation of thick-walled blood vessels lined by prominent endothelial cells, infiltration of the interstitium by chronic inflammatory cells (mainly eosinophils), and presence of lymphoid follicles with germinal centers. The patient referred for surgeon for complete excision. in this context , cases previously described in the literature, and the differential diagnosis of ALH are discussed

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Publication Date
Thu Dec 30 2021
Journal Name
Al-kindy College Medical Journal
The Impact of COVID-19 on Healthy Related Issues, A structured Review
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Coronavirus: (COVID-19) is a recently discovered viral disease caused by a new strain of coronavirus.

The majority of patients with corona-virus infections will have a mild-moderate respiratory disease that recovers without special care. Most often, the elderly, and others with chronic medical conditions such as asthma, coronary disease, respiratory illness, and malignancy are seriously ill.

    COVID-19 is spread mostly by salivary droplets or nasal secretions when an infected person coughs or sneezes.

    COVID-19 causes severe acute respiratory illness (SARS-COV-2). The first incidence was recorded in Wuhan, China, in 2019.  Since then it spreads leading to a pandemic.

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Publication Date
Wed Jun 29 2022
Journal Name
Journal Of The College Of Education For Women
Factors Affecting the Students' Choice of a Major at King Abdulaziz University
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The present study aimed at examining the factors that affect the choice of A major among a sample of BA fe(male) students at the levels 3-8 in King Abdulaziz University (KAU), in Jeddah, Saudi Arabia. To meet this objective, a descriptive survey method was used together with a questionnaire that consisted of 4 axes to answer the central question: What are the factors affecting the choice of a major at the university? Results have shown that the item that measured the students’ ability to choose the major ranked (First); it was concerned with the effect on the students' choice of his/her major in the university. On the last position and with respect to this effect came the professional tendencies and desires. Results have also shown tha

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Publication Date
Thu Oct 01 2020
Journal Name
Engineering Science And Technology, An International Journal
Thermal performance improvement based on the hybrid design of a heat sink
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Publication Date
Tue May 31 2022
Journal Name
Journal Of Positive School Psychology
A GENRE-BASED ANALYSIS OF POLITICAL SPEECHES IN THE UN GENERAL ASSEMBLY
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