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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
Thu May 21 2020
Journal Name
Journal Of Strategic Research In Social Science (josress)
A Pragmatic Study of Gender Differences in the Use of Speech Acts in Selected Suicide Notes
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DBNRSK Sayed, Journal of Strategic Research in Social Science (JoSReSS), 2020

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Publication Date
Wed Jan 01 2025
Journal Name
Science Progress
Impact of COVID-19 on the prevalence of oral and maxillofacial disorders: A retrospective cohort study
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Publication Date
Tue Nov 01 2016
Journal Name
International Journal Of Pharmaceutical Sciences Review And Research
A study on some variables affecting the preparation of ethyl cellulose based floating microspheres of lafutidine
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Lafutidine (LAF) a newly developed histamine H2-receptor antagonist with absorption window makes it a good candidate to be prepared as floating drug delivery system. The current study involves formulation and in- Vitro evaluation of lafutidine as floating microspheres. Different formulation variables that affect the physicochemical properties of the prepared microspheres besides to the drug release behavior were investigated. Fourteen formulas were prepared by emulsion (o/w) solvent evaporation method using Ethyl cellulose (EC) as the polymeric matrix and tween 80 (TW80) as an emulsifying agent. The prepared formulas were evaluated for their percentage buoyancy (%), Percentage yield (%) and Entrapment efficiency (EE %). The results obt

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Publication Date
Fri Nov 29 2019
Journal Name
Iraqi Journal Of Physics
A comparison study of the Structural and magnetic properties of pure Ni metal and NiZnMn ferrite
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The magnetic properties of a pure Nickel metal and Nickel-Zinc-Manganese ferrites having the chemical formula Ni0.1(Zn0.4Mn0.6)0.9Fe2O4 were studied. The phase formation and crystal structure was studied by using x-ray diffraction which confirmed the formation of pure single spinel cubic phase with space group (Fd3m) in the ferrite. The samples microstructure was studied with scanning electron microstructure and EDX. The magnetic properties of the ferrite and nickel metal were characterized by using a laboratory setup with a magnetic field in the range from 0-500 G. The ferrite showed perfect soft spinel phase behavior while the nickel sample showed higher magnetic loss an

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Publication Date
Sun Mar 02 2014
Journal Name
Baghdad Science Journal
We study the effect of Ultra violet rays (A-B) in treatment of Vitiligo (applied Therapy)
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This research evaluated the effect of (UV)(400-320A)Hz(320-220B)Hz on the patient with vitiligo , using it with our new combing therapy that include the oral (Psorlene ) topical , meladinine solution applied on the Vitiligiousns Lesions , In edition to the instralesnional injection in the Vitiligiousns Lesions by long acting steroid (kenacort-A ) by aprecentage of (5%) , after that we expose the patient to UV . The ruslets of this way of treatment more effective by using of the UV rays in the treatment of vitiligo , while the previous treatment that used the UV ray with or with out the psorlene , the results were not effective on controlling of the Vitiligio diseases comparing by the treatment used in this research as it stop’s the sp

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Publication Date
Sat Apr 10 2021
Journal Name
المؤتمر العلمي الدولي الثالث - المجلة الامريكية الدولية للعلوم الانسانية والاجتماعية
Public Governance and Sustainable Development - A descriptive study of the reality of public institutions in Iraq
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In light of crises, the need for efficient and flexible public administrations to make quick and decisive decisions, also institutions capable of directing the internal elements and components of them and adapting them to the requirements of rapid change due to crises and disasters, which led to scarce resources becoming scarcer and economic, political and social problems becomes more prominent. For the majority of developing countries, including Iraq, the increasing need for the importance of moving towards enhancing the efficiency of the performance of public institutions while trying to predict their future, can only be achieved. Through solid mechanisms and principles of governance that enhance the ability of institutions and make them

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Publication Date
Tue Oct 01 2019
Journal Name
Ceramics International
A first-principles study of the electronic, structural, and optical properties of CrN and Mo:CrN clusters
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Publication Date
Mon Jun 15 2020
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of dental enamel color after fixed orthodontic therapy using two types of protectors to prevent white spot lesions (A prospective clinical study)
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Background: The aim of this study is to evaluate the color change ∆E of the dental enamel following treatment with 2 kinds of protector (icon infiltrant, clinpro varnish) before fixed orthodontic treatment to avoid the possible white spot lesions. Materials and Methods: Fifty four subjects treated with fixed appliances were divided into 3 groups: the 1st group was control, while the 2nd and 3rd groups were treated with icon infiltrant and clinpro varnish before bonding procedure, respectively. Color parameters (L,a,b) were recorded for the middle and gingival thirds before and after bonding procedure to get the ∆E of each group. Results: One-way ANOVA test showed a non-significant difference in ∆E between the 3 groups a

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Publication Date
Mon Dec 30 2013
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Permeability Prediction of Un-Cored Intervals Using FZI Method and Matrix Density Grouping Method: A Case Study of Abughirab Field/Asmari FM., Iraq
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Knowledge of permeability is critical for developing an effective reservoir description. Permeability data may be calculated from well tests, cores and logs. Normally, using well log data to derive estimates of permeability is the lowest cost method. This paper will focus on the evaluation of formation permeability in un-cored intervals for Abughirab field/Asmari reservoir in Iraq from core and well log data. Hydraulic flow unit (HFU) concept is strongly related to the flow zone indicator (FZI) which is a function of the reservoir quality index (RQI). Both measures are based on porosity and permeability of cores. It is assumed that samples with similar FZI values belong to the same HFU. A generated method is also used to calculate permea

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Publication Date
Sun Jun 01 2014
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Suggested Model for The Work of the Certified Fraud Examiner & His Role in Reducing The Incidents of Fraud and Corruption: An Applied Study in The Federal Board of Supreme Audit
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Is hardly day expire without hearing the news either Abuse Managementthe accounting standards or the existence of serious misstatements by someauditors.Which caused the demanding of many companies in the recent republication of the financial statements and the re-announcement of its financialresults. Such acts raise questioning about the role that should be played by theauditors, prompting agencies responsible for setting auditing standards to takeTo throw increasingly responsibility on the auditors in order to interest risksfraud The Risks of Fraud in their review of the financial statements.also The Public Company Accounting Oversight Board in the U.S.called about the need of owning the Certified Public Accountants those whoaudits for

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