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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 Mar 15 2024
Journal Name
Journal Of Baghdad College Of Dentistry
Efficiency of osseodensification versus screw expansion technique for augmentation of narrow alveolar ridges: A comparative clinical study
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Background: Alveolar ridge expansion is proposed when the alveolar crest thickness is ≤5 mm. The screw expansion technique has been utilized for many years to expand narrow alveolar ridges. Recently, the osseodensification technique has been suggested as a reliable technique to expand narrow alveolar ridges with effective width gain and as little surgical operating time as possible. The current study aimed to compare osseodensification and screw expansion in terms of clinical width gain and operating time. Materials and methods: Forty implant osteotomies were performed in deficient horizontal alveolar ridges (3–5 mm). A total of 19 patients aged 21–59 years were randomized into two groups: the screw expansion group, which invo

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Publication Date
Fri Jan 01 2021
Journal Name
Biochemical & Cellular Archives
A COMPARATIVE STUDY ON SOME BIOCHEMICAL PARAMETERS IN INFERTILE PATIENTS.
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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Determining the Optimal Ratio of Liquidity in Iraqi Commercial Banks for period (2005-2013): applied research using Iraqi Commercial Banks as a sample study
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  This study  focused on a fundamental issue which was represented by ability of Iraqi central bank in facing the difficulty of determining  the optimal ratio of liquidity in the Iraqi banks in terms of the balancing between its obligations to the depositors and borrowers, and liquidate their funds on one hand and the risks on the other hand.the search aimed  for achieving the goals which represented by identifying the possibility of Iraqi banks to apply the regulations rules and  instructions  issued by central bank  of  Iraq in determining  ratio  of  liquidity and  its  appropriate with Iraqi  banks  action to implement  a  reasonable  profit to&

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Publication Date
Tue Jan 01 2019
Journal Name
Cpwr
Development of a workforce sustainability model for construction
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Publication Date
Sun Mar 17 2019
Journal Name
Baghdad Science Journal
The Potential of some Plant Extracts as Radical Scavengers and Dipeptidyl Peptidase-4 Inhibitors
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Seeds, beans, leaves, fruit peel and seeds of five plants (Ferula assa-foetida, Coffea robusta, Olea europaea, Punica granatum and Vitis vinifera, respectively) were extracted with four solvents (distilled water, 80% methanol, 80% acetone and a mixed solvent that included methanol, ethanol, acetone and n-butanol at proportions 7:1:1:1). Such manipulation yielded 20 extracts, which were phytochemically analyzed for total polyphenols (TP) and flavonoids (TF). The DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging activity (RSA) and DPP-4 (dipeptidyl peptidase-4) relative inhibition activity (RIA) were also assessed for each extract. The results revealed that mixed solvent extract of V.

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Publication Date
Tue Jun 15 2021
Journal Name
Al-academy
Features of the actor's performance in the ritual theater (Iraqi theater as a model): علي شخير نفل
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The features of the actor's performance in the ritual theater are of great importance and chief in theatrical work since the first emergence of the theater, as the features of the performance were embodied in all Iraqi theatrical performances, but they took personal privacy in some ritual performances because of their differences and similarities between the ritual theatrical performance and the ritual show Al-Khalis, who wanted the researcher to know the similarities and differences in the features of the ritual performance and in the theatrical performance, despite the many transformations that occurred in the theater and affected the features of the performance, but it remained an important and attractive link between the recipient, t

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Publication Date
Thu Jun 25 2020
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Evaluating the Clinical Outcomes of Three Medication Regimens for Treating a Sample of Iraqi Persistent Asthmatic patients
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Abstract

    Asthma is a complex disease defined by chronic airway inflammation and airflow limitation causing variable respiratory symptoms which include shortness of breath (SOB), wheezing, chest tightness and cough. Asthma guidelines advocate adding a second long acting bronchodilator to medium doses of inhaled corticosteroids (ICS) rather using high doses of ICS alone to control moderate to severe persistent asthma. The aim of this study was to evaluate the clinical outcomes of three medication regimens indicated for Iraqi patients suffering from persistent asthma. 

    This study was interventional randomized clinical study conducted on a sample of adult Iraqi asthm

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Publication Date
Thu Jun 25 2020
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn: 1683 - 3597 , E-issn : 2521 - 3512)
Evaluating the Clinical Outcomes of Three Medication Regimens for Treating a Sample of Iraqi Persistent Asthmatic patients
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Abstract     Asthma is a complex disease defined by chronic airway inflammation and airflow limitation causing variable respiratory symptoms which include shortness of breath (SOB), wheezing, chest tightness and cough. Asthma guidelines advocate adding a second long acting bronchodilator to medium doses of inhaled corticosteroids (ICS) rather using high doses of ICS alone to control moderate to severe persistent asthma. The aim of this study was to evaluate the clinical outcomes of three medication regimens indicated for Iraqi patients suffering from persistent asthma.      This study was interventional randomized clinical study conducted on a sample of adult Iraqi asthmatic patients in Baghdad City. The study com

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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
A study the electrical properties of a Se:2.5%as thin films prepared by thermal cvaporation
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thin films of se:2.5% as were deposited on a glass substates by thermal coevaporation techniqi=ue under high vacuum at different thikness

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Publication Date
Fri Sep 30 2022
Journal Name
College Of Islamic Sciences
TYPES OF THINKING ACCORDING TO IBN AL-QAYYIM (Analytical Thinking as a Model)
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The human intellect and his ability to complex thinking is a characteristic that Allah has given him above all his creatures. Islam came to encourage the utilization of the mind by thought, contemplation and consideration of the kingdom of Allah, His signs and religion, and He gave us a set of legislation that preserves the mind and protects it from falling into error or deviation.

This research deals with one of the most important components of civilizations in general and Islamic civilization in particular, which is thinking and what is related to it. It is an essential and influential component in man's dealing with life around him and the for

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