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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 Mar 03 2013
Journal Name
Baghdad Science Journal
A Comparison of the Methods for Estimation of Reliability Function for Burr-XII Distribution by Using Simulation.
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This deals with estimation of Reliability function and one shape parameter (?) of two- parameters Burr – XII , when ?(shape parameter is known) (?=0.5,1,1.5) and also the initial values of (?=1), while different sample shze n= 10, 20, 30, 50) bare used. The results depend on empirical study through simulation experiments are applied to compare the four methods of estimation, as well as computing the reliability function . The results of Mean square error indicates that Jacknif estimator is better than other three estimators , for all sample size and parameter values

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Publication Date
Sat Dec 20 2025
Journal Name
Bulletin Of The Iraq Natural History Museum
MORPHOLOGICAL AND MOLECULAR DESCRIPTION FOR A NEW RECORD OF NEMATODE ACROBELOIDES VARIUS KIM, KIM & PARK, 2017 (RHABDITIDA, CEPHALOBIDAE) FROM IRAQ
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This study aimed to identify and describe one of the bacterial feeder nematode Acrobeloides varius Kim, Kim and Park, 2017 (Rhabditida, Cephalobidae), which was isolated from soil samples that were collected from Baghdad, central of Iraq, and was classified using both morphological and molecular criteria. All specimens of A. varius were cultured, identified and described using morphometric criteria. Selected specimens (Zah. IRQ3 OR994579.1 isolate) of this species were characterized by having the body length of the male ranging from (184.94 – 221.72 μm), the body length of the female ranging (507.38 – 521.92 μm) and the body length of the juvenile ranging from (355.53 – 490.35 μm). Selected specimens of this species were m

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Publication Date
Wed Apr 01 2015
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
Security For Three -Tired Web Application
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Web application protection lies on two levels: the first is the responsibility of the server management, and the second is the responsibility of the programmer of the site (this is the scope of the research). This research suggests developing a secure web application site based on three-tier architecture (client, server, and database). The security of this system described as follows: using multilevel access by authorization, which means allowing access to pages depending on authorized level; password encrypted using Message Digest Five (MD5) and salt. Secure Socket Layer (SSL) protocol authentication used. Writing PHP code according to set of rules to hide source code to ensure that it cannot be stolen, verification of input before it is s

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Publication Date
Fri Nov 20 2020
Journal Name
Solid State Technology
Comparative Study for Bi-Clustering Algorithms: Historical and Methodological Notes
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Publication Date
Mon Feb 01 2021
Journal Name
Journal Of Physics: Conference Series
The Fear Effect on a Food Chain Prey-Predator Model Incorporating a Prey Refuge and Harvesting
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Abstract<p>In this paper, we investigate the impact of fear on a food chain mathematical model with prey refuge and harvesting. The prey species reproduces by to the law of logistic growth. The model is adapted from version of the Holling type-II prey-first predator and Lotka-Volterra for first predator-second predator model. The conditions, have been examined that assurance the existence of equilibrium points. Uniqueness and boundedness of the solution of the system have been achieve. The local and global dynamical behaviors are discussed and analyzed. In the end, numerical simulations are confirmed the theoretical results that obtained and to display the effectiveness of varying each parameter</p> ... Show More
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Publication Date
Mon Mar 13 2017
Journal Name
Journal Of Baghdad College Of Dentistry
A study to compare the internal fitness and marginal gap between single crowns and crowns within three-unite bridge of zirconia substructure fabricated by CAD-CAM system. (An In vitro study)
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ABSTRACT Purpose: the aim of this in vitro study was to compare the marginal gap and internal fitness between single crowns and the crowns within three-unit bridges of zirconium fabricated by CAD-CAM system. Materials and methods: A standard model from ivoclar company was used as a pattern to simulate three-units bridge (upper first molar and upper first premolar) as abutments used to fabricate stone models, eight single crowns for premolar and eight of three units bridges. Crowns and bridges fabricated by CAD-CAM system were cemented on their respective stone models then sectioned at the mid-point buccolingaully and misiodistaly and examined under stereomicroscope. Result: the marginal gap in premolar crowns and premolar within bridge we

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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
Handling a problem of transport solid waste in Baghdad City to Healthy landfill sites using transportation Model
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 A problem of solid waste became in the present day common global problem among all countries, whether developing or developed countries, and can say that no country in the world today is immuning from this dilemma which must find appropriate solutions. The problem has reached a stage that can not ignore or delay, but has became a daily problem occupies the minds of ecologists, economists and politicians took occupies center front in the lists of  priorities for the countries in terms of finding solutions to the rapid scientific and radical them. and that transport costs constitute an important component of total costs borne by the municipal districts in the process of disposal of solid waste, so any improvement in the

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Publication Date
Wed Oct 09 2019
Journal Name
Journal Of The College Of Education For Women
Silence as a Means of Communication in Harold Pinter’s The Caretaker
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Harold Pinter’s The Caretaker(1959) clearly portrays a lack of communication among the characters of the play which refers to the condition of modern man. This failure of communication led Harold Pinter to use a lot of pauses and silences in all the plays he wrote instead of words. Samuel Beckett preceded Pinter in doing so in his plays and one way to express the bewilderment of modern man during the 20th century is through the use of no language in the dramatic works. Language is no more important to modern man; instead, he uses silence to express his feelings. Silence is more powerful than the words themselves. That’s why long and short pauses can be seen throughout all Pinter’s plays.

In this play, th

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
A comparative study of the role of monetary policies in achieving economic growth in some oil and non-oil countries during the period 1990-2017
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The research problem was to identify the impact of monetary policies on economic growth in the oil and non-oil countries. The researcher chose the Republic of Iraq as an example for the oil countries and the Arab Republic of Egypt as an example for the non-oil countries to hold a comparison on the impact of monetary policies.

The research found that the monetary policies and their tools in the Iraqi economy affect the rate of GDP growth by 73%, which shows the strong impact of monetary policies on the economic growth in the Iraqi economy as an example of an oil state. GDP growth rate of 61%, indicating the impact of monetary policies on economic growth in the

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Publication Date
Tue Mar 15 2022
Journal Name
Al-academy
the indication of the scene as a symbolic system in the Iraqi theatrical
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The theatrical view reflects various connotations and intellectual and aesthetic implications, as the view includes a symbolic geometric, architectural and archetypal connotation suggestive of reality and nature, as theatrical art is the woman that reflects reality, specifically the significance of the theatrical view that reveals to us the philosophical, aesthetic and cognitive dimensions of theatrical trends, so the research came with the methodological framework, which It included the research problem (what is the significance of the scene as a symbolic system in the Iraqi theatrical performance), the importance of the research and the need for it, the research objective, the limits of the research and the most important terms.
A

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