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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 Apr 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Rainwater Drainage Service Improvement Using a Number Of Quality Tools at the Directorate of Karbala Sewage
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The basic objective of the research is to study the quality of the water flow service in the Directorate of Karbala sewage and how to improve it after identifying the deviations of the processes and the final product and then providing the possible solutions in addressing the causes of the deviations and the associated quality gaps. A number of quality tools were used and applied to all data Stations with areas and activities related to the drainage of rainwater, as the research community determines the stations of lifting rainwater in the Directorate of the streams of Karbala holy, and the station was chosen Western station to apply the non-random sampling method intended after meeting a number of. It is one of the largest and m

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Publication Date
Sun Dec 07 2008
Journal Name
Baghdad Science Journal
Improvement of the monochrome image hologram by using a random phase and increasing number of Samples
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This paper present a study about effect of the random phase and expansion of the scale sampling factors to improve the monochrome image hologram and compared it with previous produced others. Matlab software is used to synthesize and reconstruction hologram.

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Publication Date
Wed Apr 15 2020
Journal Name
Journal Of Engineering Science And Technology
INFLUENCE OF A RIVER WATER QUALITY ON THE EFFICIENCY OF WATER TREATMENT USING ARTIFICIAL NEURAL NETWORK
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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Generating a Strong Key for a Stream Cipher Systems Based on Permutation Networks
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The choice of binary Pseudonoise (PN) sequences with specific properties, having long period high complexity, randomness, minimum cross and auto- correlation which are essential for some communication systems. In this research a nonlinear PN generator is introduced . It consists of a combination of basic components like Linear Feedback Shift Register (LFSR), ?-element which is a type of RxR crossbar switches. The period and complexity of a sequence which are generated by the proposed generator are computed and the randomness properties of these sequences are measured by well-known randomness tests.

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Publication Date
Sun Mar 15 2020
Journal Name
Al-adab Journal
The Study and Analysis Grammatical of verbal sentence a fragment of "Zurita" (Leopoldo alas Clarín)
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This article deals with the study of theories about verbal periphrasis as a grammatical construction; the aim of this point it offers good and valid guidelines to improve the linguistic description. The interest in the subject comes from its importance in the process of language teaching for the students of Spanish and to clarify this type of curriculum of this research we analyzed a literary text. From "Zurita"

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Publication Date
Wed Jun 03 2015
Journal Name
Al-ustath
Witchcraft and Women’s Spaces; A cultural Materialism Study of John Updike’s The Witches of Eastwick
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Witch stories are part of American popular culture, and this culture is extremely influenced by a continuing reliance on its past. The modern obsession of Americans with witches, whether real or metaphorical, is related to politics especially when it came to issues of gender politics. This article exposes a modern image of the female character seen from a male author point of view. John Updike, influenced by the changes that happened to women within second wave of feminism, attempted to write The Witches of Eastwick (1984). Actually, he presented women who did have a sort of careers. His witches are professional active and dynamic. What do witches stand for in American Culture? Why did Updike choose to write

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Publication Date
Mon Aug 18 2025
Journal Name
Al-mustansiriyah Journal Of Science
Epidemiological Study to Investigate a Possible Vector of Visceral Leishmaniasisin the Central Region of Iraq
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An epidemiological study in Al-Mahmmodiya (50 km south Baghdad) to investigate a possible vector of Leishmaniasis were applied .This region is considered as a foci of Leishmaniasisaccording to the health association statistics. CDC light traps were used to collect the insects nightly. Insects were collected by Indoor application as human dwellings and animal shelters and Outdoor application as rodent's barrows and field trees. Sand flies were transported to the laboratory, isolated and identified according to the identification keys in Tropical Biological Researches Unit at the Collage of Science / University of Baghdad. Must of the collected sand flies were belonging to three species PhlebotomuspapatasiScopoli(45%), PhlebotomusalexandriSin

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
Water harvesting and sustainable spatial development A case study of the province of badra – zurbatiyah
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The major climate changes that have affected the planet in addition to wave the big drought plaguing the study area, including the lack of water for imports Badra River fatigue because of the Iran constructing dams on this river and make use of the waters for the benefitof its territory. The subject of finding sources of water has become available with the possibility of exploiting them in an exemplary manner is one of the key things in order to be exploited somewhere.
The study area was chosen within the eastern border of the province of Wasit within the district of Badra border, an area of (1557.5 km2) almost "to study the characteristics of hydrological and identify possibilities for water harvesting them. In this study was conduct

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Publication Date
Sat Jun 01 2024
Journal Name
Iraqi Journal Of Physics
A Study the Addition of Silver Dioxide on Some Optical Properties of Phosphate Bioactive Glass
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This study investigates the influence of silver oxide (Ag2O) concentration on the optical characteristics of phosphate bioactive glasses (PBGs). PBGs have emerged as promising alternatives to conventional silicate glasses in the medical field due to their excellent bioactivity and chemical resistance. Samples with varying Ag2O concentrations (0, 0.25, 0.5, and 0.75g) were sintered at 780°C for 2 hrs in an electric furnace. The samples were subjected to Fourier transfer infrared spectroscopy (FTIR), ultraviolet-visible (UV-Vis) spectroscopy, and photoluminescence (PL) tests to assess their functional groups and optical properties. By analyzing the FTIR spectrum of phosphate bioactive glass containing different amounts of Ag2O, it is

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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
Crisis management effective of business organizations in the era of managerial technique: a philosophical study
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At a time of increasing human potential in the face of crises and risks through the use of technology on a large scale and steadily in various fields of life, and the vulnerability of business organizations as a result of mistakes. The failure of a sudden these errors or omissions or symptoms. Also, some crises occur outside the control of management, others caused by leakage of important information and sometimes secret may be a strategy or a new plan or new project occurs outside the organization to the opposite of what is planned. Therefore, the crisis management are critical to all organizations, because the active management of the crisis helps to ensure the continued prosperity of the organization. Here comes from the resea

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