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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
Mon Jun 28 2021
Journal Name
Journal Of Engineering
Effective quality control of a municipal wastewater treatment plant using Geographic information systems: A Review
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Inefficient wastewater disposal and wastewater discharge problems in water bodies have led to increasing pollution in water bodies.  Pollutants in the river contribute to increasing the biological oxygen demand (BOD), total suspended solids (SS), total dissolved solids (TDS), chemical oxygen demand (COD), and toxic metals render this water unsuitable for consumption and even pose a significant risk to human health. Over the last few years, water conservation has been the subject of growing awareness and concern throughout the world, so this research focused on review studies of researches that studied the importance of water quality of wastewater treated disposal in water bodies and modern technology to management w

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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Requirements of investment in the marsh : a case study in the Marshlands of Maysan
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The search aims to find out the most important requirements for the success of marshes investment and maximize the expected returns of investment was marked by a problem find aquestion for availability requirements necessary for the success of marshes investment has a research community owners decision in the province Maysan the most important conclusions to the search is that the investment great importance in support of the economy and raising the cultural and social level, there is no investment successful but only with configure the investment environment appropriate economic, social, cultural, political, and security ways. the most important recommendations are working on the provision of the investment environment appropria

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Publication Date
Sun Feb 17 2019
Journal Name
Iraqi Journal Of Physics
A study of the solvent effect on the low temperature spectra of benzoanthracene molecules
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been taken at room temperature down to liquid nitrogen temperature (77K). Polar and nonpolar solvents have been used to study the solvent effect on the absorption and fluorescence spectra of solute molecules. Some of the spectroscopic parameters have been determined as functions of solvent polarity and temperature. The results indicate that the band width FWHM increases with increasing the solvent polarity and temperature, while the peak emission cross section decreases with increasing of solvent polarity and decreases with increasing the temperatures. Clear vibrational structure spectra of benzoanthracene molecules have been observed in Nonane and Hexane solvents at 77K.

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
What came as a language in the book to explain Ibn Aqeel on Alfiya Ibn malek
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It is found in the book "Ibn Aqeel: Alfiya Ibn Malek" that there are some linqustical aspected are related to the native tribal speakers like Tamim or Tie or some others. Sometimes in the book he said "some Arabian said without mentioning the name of the tribe.
As weel, he hasn’t mentioned the accent but he does mention the language. In the book, he has brought back the most important and the biqqest Arabian tribes suchas tribes of Hegaz, Tamim, Hatheyal, son of Anber, Tie, Rabia Bin Wael, Bani Katham, Au there, Bani AL Harth, Bani Kalb, Bani Hgim, Zabid, Hamedan, Alia Qais, Bani Ameer and many others. However, the most mentioned tribes were Hegaz and Tami.
Hence, the importance of the book expiain Ibn Aqeel by mentioning these A

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Publication Date
Wed Mar 09 2022
Journal Name
Journal Of Craniofacial Surgery
The Use of Osseodensification for Ridge Expansion and Dental Implant Placement in Narrow Alveolar Ridges: A Prospective Observational Clinical Study
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The osseodensification (OD) drilling technique was suggested as an alveolar ridge expansion technique, so the aim of this prospective clinical study was to evaluate the amount of bone expansion obtained by the OD drilling technique and its effect on implant stability in patients with narrow alveolar ridges. The width of the alveolar ridge was measured at the crest before and after implant site preparation, whereas the implant stability was measured using Osstell Beacon implant stability quotient (ISQ). The ISQ values were recorded immediately postoperatively and after 16 weeks. Twenty-three patients were included; they received 40 implants. The mean (± standard deviation [SD]) amount of expansion was 1.29 (± 0.41) mm, and the difference b

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Publication Date
Wed Oct 26 2022
Journal Name
Petroleum Science And Technology
Building 3D geological model using non-uniform gridding for Mishrif reservoir in Garraf oilfield
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Publication Date
Fri May 05 2023
Journal Name
International Journal Of Professional Business Review
The Effect of Emotional Intelligence on Manager Performance: a Field Study in the General Authority for Irrigation and Reclamation Projects in Baghdad
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Purpose: the purpose of this study is to investigate how managers working for the General Authority for Irrigation and Reclamation Projects react to the impact of Emotional Intelligence (EI) on their performance.   Theoretical framework: The current study includes an intellectual framework on two variables, namely EI and Manager Performance (MP), because it is essential to investigate the relationship between these two variables and the impact of EI on MP.   Design/methodology/approach: The research problem is that a manager's capacity to make wise decisions about their work or interactions with subordinates is diminished when they have inadequate EI. The questionnaire is used as a tool for gathering data for the study, and the st

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Publication Date
Tue Oct 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Solution of Fuzzy Maximal Flow Problems of Vehicles in Province of Diwaniyah Using the Ranking Function for Fuzzy Linear Programming Model
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Abstract

The traffic jams taking place in the cities of the Republic of Iraq in general and the province of Diwaniyah especially, causes return to the large numbers of the modern vehicles that have been imported in the last ten years and the lack of omission for old vehicles in the province, resulting in the accumulation of a large number of vehicles that exceed the capacity of the city's streets, all these reasons combined led to traffic congestion clear at the time of the beginning of work in the morning, So researchers chose local area network of the main roads of the province of Diwaniyah, which is considered the most important in terms of traffic congestion, it was identified  fuzzy numbers for

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Publication Date
Thu Mar 30 2023
Journal Name
College Of Islamic Sciences
The effect of readings on the multiplicity of explanatory significance of a single Qur’anic word, a study through the interpretation of Ibn Attia al-Andalusi
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The study aimed to clarify the meanings learned and inferred from reading books، letters and messages in Surat Al-Qur’an. The inductive method، the analytical method، and the deductive method، One of the most prominent results of the research: that the multiplicity of Qur’anic readings produces a variety and expansion in the meaning that has a clear impact on the interpretation by clarifying the meaning of the verse.

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Publication Date
Thu Dec 20 2007
Journal Name
Journal Of Planner And Development
To contribute in handling the housing crisis in the city of BaghdadA study for the decision of the Mayoralty of Baghdad to allow adding a third floor for the residential units
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We need to know the basic facts concerning planning top and bottom limits including any critical levels or the threshold over which the cost would be much higher for land development. Therefore this paper concerned with Baghdad Municipality decision No.2/1004 dated 7/12/2004. The reason behind this decision is the hope to face up at least in the severe housing crisis in the city of Baghdad. This paper attempts to know the attitude of the local community in the general through a field study of people living near such dwelling where third floors are added of. This might indicate any positive or negative effects whether on short or long-term including its effect on the theoretical side including the population growth of Baghdad, the

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