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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 Jul 01 2025
Journal Name
South African Journal Of Chemical Engineering
Expired azithromycin and cephalexin as corrosion inhibitors for aluminum in saline-acidic solution
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Publication Date
Fri Apr 01 2022
Journal Name
Baghdad Science Journal
Iron (II) Determination in Lipstick Samples using Spectrophotometric and Microfluidic Paper-based Analytical Device (µPADs) Platform via Complexation Reaction with Iron Chelator 1, 10-phenanthroline: A Comparative Study
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This study was undertaken to introduce a fast, accurate, selective, simple and environment-friendly colorimetric method to determine iron (II) concentration in different lipstick brands imported or manufactured locally in Baghdad, Iraq. The samples were collected from 500-Iraqi dinars stores to establish routine tests using the spectrophotometric method and compared with a new microfluidic paper-based analytical device (µPAD) platform as an alternative to cost-effective conventional instrumentation such as Atomic Absorption Spectroscopy (AAS). This method depends on the reaction between iron (II) with iron(II) selective chelator 1, 10-phenanthroline(phen) in the presence of reducing agent hydroxylamine (HOA) and sodium acetate (NaOAc) b

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Publication Date
Thu Dec 30 2021
Journal Name
Journal Of Legal Sciences
Violation of the rights of sound record producers (piracy) (A Comparative study)
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Piracy is one of the most important problems faced by sound record producers, because it is a problem that technology, evolves with the development of time and and although piracy is not a new problem, it has received great attention in recent years, because of the means by which (the Internet) and its size result from it, even In many of the ruler, describing it as (the crime of nd she participated in the great the electronic age) aharm it causes to all the groups involved in it producing the sound recording, because there are three categories that contribute to the production of the sound recording, which is (the author of the recorded work, the st who performs the work and the producer who artiperforms an operation Performance recording

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Publication Date
Sat Jun 19 2021
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
The Role of Ginkgo biloba Extract as Monotherapy in Improving the Outcomes of Patients with Metabolic Syndrome: A Pilot Comparative Study with Metformin
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The present study evaluates the effects of Ginkgo biloba extract as monotherapy on the glycemic status, insulin resistance (IR), body mass index (BMI), and visceral adiposity index (VAI), in addition to the inflammatory markers, oxidative status and leptin level in patients with metabolic syndrome in comparison with metformin.

The study is a randomized, double-blind pilot study conducted during the period May to September, 2020. Fifty patients were recruited in the study and they were allocated into two groups (25 per each group): Ginkgo biloba and Metformin groups, they received (120 mg Ginkgo biloba extract/ capsule) and (500 mg Metformin/ capsule) respectively; orally as a single dose for 90 days. Blood samples were taken at z

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Publication Date
Sun Sep 30 2012
Journal Name
Al-hiqouq
Maintenance Contract - A Comparative Study with Islamic Jurisprudence
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Contemporary life is racing against time in its temptations and variables, and it has become shaped and changed in an amazing way in its various aspects and fields. This was facilitated by intellectual and scientific communication between civilizations, and the rapid progression in successive inventions and discoveries in the fields of science and arts of knowledge. This contributed to a great economic and commercial renaissance. Then, these economic developments entered the world into a very strong competition, which forced producers to calculate all production costs, to reach the highest profits by reducing the price of the produced commodity on the one hand, and achieving quality in appearance (especially) on the other hand. Since the ma

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Publication Date
Tue Feb 01 2022
Journal Name
Int. J. Nonlinear Anal. Appl.
Computer-based plagiarism detection techniques: A comparative study
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Plagiarism is becoming more of a problem in academics. It’s made worse by the ease with which a wide range of resources can be found on the internet, as well as the ease with which they can be copied and pasted. It is academic theft since the perpetrator has ”taken” and presented the work of others as his or her own. Manual detection of plagiarism by a human being is difficult, imprecise, and time-consuming because it is difficult for anyone to compare their work to current data. Plagiarism is a big problem in higher education, and it can happen on any topic. Plagiarism detection has been studied in many scientific articles, and methods for recognition have been created utilizing the Plagiarism analysis, Authorship identification, and

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Publication Date
Thu Dec 15 2022
Journal Name
Al-academy
The functional diversity of the directorial vision in the political theater cinema as a model
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It is very necessary for the political theater to be within the space of every theatrical performance, so that the theater carries the diverse and enlightened values and cultures of this world. political theatre. In the first chapter, the researcher dealt with (the methodological framework), which includes the research problem identified by the researcher with the following question (the functional diversity of the directorial vision in the political theater)
Importance, purpose, limits and seal by defining terminology.
In the second chapter, the researcher dealt with the theoretical framework on two topics, the first (transformations of directorial vision in theatrical performance) and the second topic (aesthetic experiences i

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Publication Date
Thu Nov 03 2022
Journal Name
Res Militaris
Prose of Sons of Imam Ali Al-Rida (Peace Be Upon Them): A Study Regarding the Structure of the Image and Its Implications - Simile as a Model
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Praise be to God, Lord of the Worlds, and prayers and peace be upon the most honorable of creation, Muhammad, whom God sent as a mercy to the worlds, and his pure God and his faithful companions. The Islamic heritage was replete with texts issued from among the pure infallibility, which constituted a prominent teacher that takes the student to stop there in search of its goals, purposes and beauty. The choice was made from those texts that were issued by the imams of Muslims in the Abbasid era, namely Imam Muhammad al-Jawad, his son Imam Ali al-Hadi and his grandson Imam Hassan Zaki al-Askari. (Peace be upon them), and scholars have called them (sons of satisfaction), and researchers have shed light on these texts from rhetorical, artistic

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Publication Date
Mon Jul 28 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Photogrammetric analysis of facial soft tissue profile of Iraqi adults sample with Class II div.1 and Class III malocclusion: (A comparative study)
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Background: The purposes of this study were to determine the photogrammetric soft tissue facial profile measurements for Iraqi adults sample with class II div.1 and class III malocclusion using standardized photographic techniques and to verify the existence of possible gender differences. Materials & methods: Seventy five Iraqi adult subjects, 50 class II div.1 malocclusion (24 males and 26 females), 25 class III malocclusion (14 males and 11 females), with an age range from 18-25 years. Each individual was subjected to clinical examination and digital standardized right side photographic records were taken in the natural head position. The photographs were analyzed using AutoCAD program 2007 to measure the distances and angles used in t

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Publication Date
Sat Oct 28 2023
Journal Name
Baghdad Science Journal
COMPARATIVE STUDY BETWEEN A NOVEL DETERMINISTIC TEST FOR MERSENNE PRIMES AND THE WELL-KNOWN PRIMALITY TESTS
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In this article, a new deterministic primality test for Mersenne primes is presented. It also includes a comparative study between well-known primality tests in order to identify the best test. Moreover, new modifications are suggested in order to eliminate pseudoprimes. The study covers random primes such as Mersenne primes and Proth primes. Finally, these tests are arranged from the best to the worst according to strength, speed, and effectiveness based on the results obtained through programs prepared and operated by Mathematica, and the results are presented through tables and graphs.

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