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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
Tue Jan 01 2019
Journal Name
Cpwr
Development of a workforce sustainability model for construction
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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
Thu Apr 01 2021
Journal Name
Journal Of Molecular Structure
Mixed-ligand complexes of ampicillin derived Schiff base ligand and Nicotinamide: Synthesis, physico-chemical studies, DFT calculation, antibacterial study and molecular docking analysis
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A novel series of mixed-ligand complexes of the type, [ML1(L2)3]Clx [M= Cr(III), Fe(III), Co(II),Ni(II), Cu(II), Cd(II) and Hg(II), n = 2, 3], was synthesized using Schiff base (HL1) as main ligand, nicotinamide (L2) as secondary ligand, and the corresponding metal ions in 1:3:1 molar ratio. The main ligand, HL1 was prepared by the interaction of ampicillin drug and 4-chlorobenzophenone. The synthesized mixed ligand complexes were characterized by elemental analysis, UV-Vis, FT-IR,1H-NMR,13C-NMR and TG/DTG studies. In the mixed-ligand complexes, the Schiff base ligand, HL1 showed coordination to the central metal ion in tridentate manner via azomethine nitrogen, β-lactam ring oxygen and deprotonated carboxylic oxygen atoms, whereas the sec

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Publication Date
Fri Jan 01 2021
Journal Name
Journal Of Economics And Administrative Sciences
The influence of organizational culture on the organizational performance of educational institutions (University of Technology as a model)
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The organizational culture is an effective control mechanism that dictates the behavior of employees and according to their intellectual and social orientations, so it is considered a more powerful way to control employee orientations and determine their management according to organizational rules and regulations, as it was one of the most important factors determining the performance of organizations, while organizational performance is a measure of what the organization has achieved from the objectives of the scheme To ensure that it faces various changes and remains within the global competition, and to reach that it was necessary to identify the most prominent and most important research problems in knowing the extent of com

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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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Publication Date
Wed Jul 01 2015
Journal Name
Al–bahith Al–a'alami
The Position of the Oil Press about the World Oil Industry / OAPEC Bulletin 2011-2012 as a Model
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This research deals with the attitude of oil press towards oil industry in the world and the extent of their concerns with the stages of oil industry relating to the abundance of oil and natural gas, as it is an international strategic and complementary industry. The researcher uses the survey method for content analysis of the initial article and the press news for two: years (2011-2012). The results if the study are as follows
1- Oil press is concerned with developing and the stages of the Arabic oil industry in the interest of OAPEC in the first place.
2- It is concerned with exploring, extracting, and marketing oil in the first place, then with refining operations in refineries and petrochemical plants in the second place, an

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Publication Date
Sun Jun 02 2019
Journal Name
Baghdad Science Journal
Estimating the Reliability Function of (2+1) Cascade Model
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This paper discusses reliability R of the (2+1) Cascade model of inverse Weibull distribution. Reliability is to be found when strength-stress distributed is inverse Weibull random variables with unknown scale parameter and known shape parameter. Six estimation methods (Maximum likelihood, Moment, Least Square, Weighted Least Square, Regression and Percentile) are used to estimate reliability. There is a comparison between six different estimation methods by the simulation study by MATLAB 2016, using two statistical criteria Mean square error and Mean Absolute Percentage Error, where it is found that best estimator between the six estimators is Maximum likelihood estimation method.

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Publication Date
Tue Dec 22 2020
Journal Name
Collaboration And Integration In Construction, Engineering, Management And Technology
A Hybrid Conceptual Model for BIM Adoption in Facilities Management: A Descriptive Analysis for the Collected Data
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Publication Date
Tue Jun 15 2021
Journal Name
Al-academy
The Physical Performance Of The Actor Within The Shows Of Anas Abdul Samad ( the play silence as the cry as a model): حليم هاتف جاسم
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The body has the ability to effect the audience in the the theatrical show , since he or she is transmitter , sender , seen and viewer of the humanitarian discourse as well the the images and connotations of the theatrical show, it is a tool of communication that substitutes for millions of spoken words, the modern schools of direction focused on the body language of the actor and gave it prominence in depicting facts by different connotations. The researcher studies the physical performance of the actor throughout focusing on the connotational dimensions of the body within the theatrical show , as well as the positioning of performative body within the modern schools of direction depending on the theatrical show (Rebuke ) of the Iraqi d

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Publication Date
Mon Aug 01 2022
Journal Name
Baghdad Science Journal
The Patterns of Poisoning Exposure in Different Ages in Duhok Governate: A three Years Study (2016, 2017, 2018)
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Poisoning with toxic substances accidently or deliberately can be life threatening and especially in some countries that lack the essential tests and facilities to identify the types and causes of these toxic substances. In Iraq, as many other countries, poisoning is one of the chronic public health problems. However, very little literature about the pattern of poisoning cases, types and age is available in Duhok Governorate. Therefore, this study was conducted to determine the most common patterns of poisoning and the related age and gender in Duhok Governorate from 2016-2018, which would possibly contribute to the early diagnosis and treatment of poisoning. The present study was conducted for three years, started from 1st of

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