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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 Jun 30 2019
Journal Name
Journal Of The College Of Education For Women
The Aesthetic of the Textual Interferences in the Poetry of the Ghawani's" A Miracle Nice of your Imagination as a symbol"
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     إنّ التّأمّل في الدّراسات الأدبيّة النّقديّة الحديثة الّتي تنظر إلى النّصّ أنّه لوحة تتشكّل من مجموعة تداخلات نصّيّة سابقة للنصّ المُنتج أو مُعاصرة له، تدفع القارئ إلى الغوص في أعماق النّصوص وتحليلها والكشف عن الآليّات والإجراءات الّتي اعتمدت في إنتاجه، وإظهار الجماليّات الفنّيّة التي شكلت في مُجملها كائنا حيّا يُعبّر عن حالات إنسانيّة مُستمرة الحدوث رغم تقادم الأزمان.

فالبحث هذا يعمد

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Publication Date
Fri Dec 02 2022
Journal Name
Nankai Business Review International
Evaluating the dimensions of strategic intent according to the Hamel and Prahalad model/a case study in Oil Projects SCOP Company
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Purpose

The purpose of this study is to examine the dimensions of strategic intent (SI; see Appendix 1) according to the Hamel and Prahalad model as a building for the future, relying on today’s knowledge-based and proactive strategic directions of management as long-term and deep-perspective creative directions, objective vision and rational analysis, integrative in work, survival structure and comprehensiveness in perception.

Design/methodology/approach

The quantitative approach was used based on research, detection and proof, as data were collected from leader

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Publication Date
Tue Jan 01 2019
Journal Name
Ieee Access
Implementation of Univariate Paradigm for Streamflow Simulation Using Hybrid Data-Driven Model: Case Study in Tropical Region
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Publication Date
Sat Jun 01 2024
Journal Name
University Of Thi-qar Journal Of Agricultural Research
A comparative histological, histometrical and hormonal study between the ovary and uterus of non-pregnant and pregnant local breed cat (Catus felius)
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Samples of the ovary and uterus of local breed cats used to investigate the histological, histometrical and hormonal features. The paraffin embedding technique was used for processing of tissue that stained by hematoxyline and eosin stain, and massons trichrom stain. Ovary of at proestrus or oestrus phases composed of outer cortex that covered by cuboidal germinal epithelium and inner medulla. Tunica albuginea composed of a thin layer of characterized by fusiform stromal cells. The cortex content groups of Oogonial cells, numerous primordial follicles, little primary, secondary and tertiary follicles in addition for 1-2 follicular cysts and mature corpus letium. In pregnant cat the thickness of ovarian cortex was significantly incre

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Publication Date
Fri Dec 14 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Evaluation of Quality of Primary Health Care Services at Primary Health Care Centers in Baghdad City: A Comparative Study
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Objective(s): To evaluate primary health care services at primary health care centers in Baghdad City and to compare between these primary health care centers relative to such quality. Methodology: A descriptive design, using the evaluation approach, is study to Evaluation of quality of primary care services at primary health care centers in Baghdad City. A multistage probability sample of (36) health care centers was selected. The sample consists of (12) model centers, (12) urban centers, and (12) rural centers.A constructedquestionnaire is composed of (23) items. It consisted of (5) parts that include inta

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Publication Date
Fri Sep 30 2022
Journal Name
College Of Islamic Sciences
Historical development of Islamic jurisprudence - Develop a model
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       Praise be to God, and prayers and peace be upon our master Muhammad, the Messenger of God, and upon his family, companions, and those who are guided by his guidance.

Then:

       Our Islamic jurisprudence and its basic principles are fixed, namely: the Noble Qur’an, then the Prophet’s Sunnah, then consensus, then analogy. However, it is characteristic of what makes it developed to meet the requirements of renewed life, including: sent interests, custom, approval, blocking pretexts, changing times. That is why it went through different stages, growth, brilliance, stagnation and endowment; Therefore, many scholars of Islamic jurisprudence divided its stages into four sections: the stage of inf

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Publication Date
Wed Apr 12 2017
Journal Name
Journal Of Engineering
Cultivation of Chlorella Vulgaris Using Airlift Photobioreactor Sparged with 5%CO2-Air as a Biofixing Process
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The present paper addresses cultivation of Chlorella vulgaris microalgae using airlift photobioreactor that sparged with 5% CO2/air. The experimental data were compared with that obtained from bioreactor aerated with air and unsparged bioreactor. The results showed that the concentration of biomass is 0.36 g l-1 in sparged bioreactor with CO2/air, while, the concentration of biomass reached to 0.069 g l-1 in the unsparged bioreactor. They showed also that aerated bioreactor with CO2/air gives more biomass production even the bioreactor was aerated with air. This study proved that application of sparging system for cultivation of Chlorella vulgaris microalgae using either CO2/air mixture or air has a significant growth rate, since the biorea

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Publication Date
Sun Jan 01 2023
Journal Name
Aip Conference Proceedings
Determination of paracetemol in pharmaceutical preparations samples by spectrophotometer using meta phenylenediamine as a chromogenic agent
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Publication Date
Sun Jun 03 2012
Journal Name
Baghdad Science Journal
Batch and Flow-Injection Spectrophotometric Determination of Thymol Using Procaine Hydrochloride as a New Chromogenic Reagent
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New, simple and sensitive batch and Flow-injecton spectrophotometric methods for the determination of Thymol in pure form and in mouth wash preparations have been proposed in this study. These methods were based on a diazotization and coupling reaction between Thymol and diazotized procaine HCl in alkaline medium to form an intense orange-red water-soluble dye that is stable and has a maximum absorption at 474 nm. A graphs of absorbance versus concentration show that Beer’s law is obeyed over the concentration range of 0.4-4.8 and 4-80 µg.ml-1 of Thymol, with detection limits of 0.072 and 1.807 µg.ml-1 of Thymol for batch and FIA methods respectively. The FIA procedure sample throughput was 80 h-1. All different chemical and physical e

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Publication Date
Tue Feb 01 2022
Journal Name
Macromolecular Symposia
Synthesis of 5‐Fluorouracil–Naproxen Conjugates as a Mutual Prodrug for Targeting Cancer Tissues
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Abstract<p>A new 5‐fluorouracil–naproxen conjugate is synthesized as a mutual prodrug for targeting cancer tissues. The structure of the target compound and their intermediate are characterized by their melting point, IR, <sup>1</sup>H NMR, <sup>13</sup>C NMR, and elemental microanalysis. The cytotoxic activity is preliminarily evaluated using nonsmall lung cancer CRL‐2049, human breast cancer CAL‐51, and one type of normal cell line; rat embryo fibroblast cell line. The synthesized compound shows a good cytotoxic effect at the cancer cell and no significant effect at rat embryo fibroblast cell line.</p>
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