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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 Oct 20 2024
Journal Name
Engineering Reports
A Theoretical and Experimental Investigation of the Effects of Inverted Wings Modifications on the Stability and Aerodynamic Performance of a Sedan Car at Cornering
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ABSTRACT<p>This research examines the impact of cornering on the aerodynamic forces and stability of a Nissan Versa (Almera) passenger sedan car by introducing novel modifications. These modifications included single inverted wings with end plates as a front spoiler, double‐element inverted wings with end plates as a rear spoiler, and incorporating the ground as a diffuser under the car trunk. The goal is to enhance the performance and stability of conventional passenger cars. To ensure the accuracy of the numerical data, the study utilized multiple methodologies to model the turbulence model, ultimately selecting the most suitable option. This involved comparing numerical data with wind tunnel experimental d</p> ... Show More
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Publication Date
Mon Oct 22 2018
Journal Name
Journal Of Economics And Administrative Sciences
Leadership crisis and environmental pressures A Survey of the views of a sample of administrative leaders at Mosul University and the North technical University
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The administrative leadership relies on a variety of behavioral paths in the functional areas in which it operates, and thus indicates its ability and thus has the upper hand in the organizational events, and in such a way that it can draw lessons and evaluate the results so as to test the expectations within the framework of the changes.

Does the study sample leadership have the characteristics that enable it to contain both crises and environmental stresses?

The aim of the study was to determine the location of the administrative leaders in the system of the study sample from the issue of crises and environmental pressures. The study concluded with a number of conclusions, the m

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Publication Date
Mon Mar 09 2026
Journal Name
Opción: Revista De Ciencias Humanas Y Sociales, Issn 1012-1587, Nº. 89, 2019
The effectiveness of employing the molecular representation strategy in the development of information Generation skills in the chemistry of second grade students in Intermediate School
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Autoría: Jehan Faris Yousif. Localización: Opción: Revista de Ciencias Humanas y Sociales. Nº. 89, 2019. Artículo de Revista en Dialnet.

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Publication Date
Sat Jun 08 2024
Journal Name
Karbala International Journal Of Modern Science
Designing of Human Serum Albumin Nanoparticles for Drug Delivery: a Potential Use of Anticancer Treatment
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Human serum albumin (HSA) nanoparticles have been widely used as versatile drug delivery systems for improving the efficiency and pharmaceutical properties of drugs. The present study aimed to design HSA nanoparticle encapsulated with the hydrophobic anticancer pyridine derivative (2-((2-([1,1'-biphenyl]-4-yl)imidazo[1,2-a]pyrimidin-3-yl)methylene)hydrazine-1-carbothioamide (BIPHC)). The synthesis of HSA-BIPHC nanoparticles was achieved using a desolvation process. Atomic force microscopy (AFM) analysis showed the average size of HSA-BIPHC nanoparticles was 80.21 nm. The percentages of entrapment efficacy, loading capacity and production yield were 98.11%, 9.77% and 91.29%, respectively. An In vitro release study revealed that HSA-BIPHC nan

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Publication Date
Thu Dec 31 2020
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
SYNTHESISAND STUDY OF THE COMPLEXES OF: N-(3,4,5-TRIMETHOXY PHENYL)-N- BENZOYL THIOUREA (TMPBT) WITH A NUMBER OF TRANSITION METALS AND THEIR INDUSTRIAL AND MEDICAL IMPORTANCE: SYNTHESISAND STUDY OF THE COMPLEXES OF: N-(3,4,5-TRIMETHOXY PHENYL)-N- BENZOYL THIOUREA (TMPBT) WITH A NUMBER OF TRANSITION METALS AND THEIR INDUSTRIAL AND MEDICAL IMPORTANCE
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This paper performance for preparation and identification of six new complexes of a number of transition metals Cr (lII), Mn (I1), Fe (l), Co (II), Ni (I1), Cu (Il) with: N - (3,4,5-Trimethoxy phenyl-N - benzoyl Thiourea (TMPBT) as a bidentet ligand. The prepared complexes have been characterized, identified on the basis of elemental analysis (C.H.N), atomic absorption, molar conductivity, molar-ratio ,pH effect study, I. Rand UV spectra studies. The complexes have the structural formula ML2X3 for Cr (III), Fe (III), and ML2X2 for Mn (II), Ni (II), and MLX2 for Co (Il) , Cu (Il).

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Publication Date
Sun Mar 28 2021
Journal Name
Journal Of The College Of Education For Women
The Phenomenon of Phonological Follow in Al-Amali Abi Ali Al-Qali’s Book (seq.356 Hijri): A Phonological Study: هند فاضل عباس
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This research discusses the verbal follow phenomenon in Al-Amali Abi Al-Qali’s book (seq.356 Hijri). It aims to limit the examples of this phenomenon in the book, and  examine it phonologically. Accordingly, the researcher adopted the analaytical descriptive approach, taking into account Al-Rawi’s letter when ordering the verbal follow-based examples, and the order they took in the book in question. The purposes behind this phonological study of verbal follow in Al-Amali’s book are to: reach the sounds which Arabs prefer in the process of following, confirm different beautiful and desirable senses, have easy and speedy pronunciation, maintain harmony between adjacent sounds, count the sounds that occur at the beginning of the

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Publication Date
Wed Nov 01 2023
Journal Name
Clinical Epidemiology And Global Health
The association of interleukin-10 single nucleotide polymorphisms (rs1800871) and serum levels in Iraqi patients with celiac disease: A case-control study
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Publication Date
Wed Jul 05 2017
Journal Name
International Journal Of Science And Research (ijsr)
Pacifier Sucking Habit and its Relation to Dental Caries and Type of Feeding Habits among Group of Children (Comparative Study)
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Publication Date
Sun Sep 04 2016
Journal Name
Baghdad Science Journal
Comparative Study of Grains, Flours and Baking Quality of Wheat Cultivar (Uruq) with Other Wheat Cultivars (Triticumaestivum L.) in Iraq
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The grain hardness, wet and dry gluten contents, protein and ash contents are determined in grains from different cultivars of wheat which are important in food products, either which are present in raw materials or in final products. Wheat is also a very important food raw material, and flour as the final product of milling. The importance of knowing the physical and chemical properties of wheat and flour is due to the determination of quality and kind of flour which is produced after the milling process. In this work, some physical and chemical properties of different wheat cultivars are determined and the comparisons of these characteristics are performed in both wheat and flour. Uruq Wheat sample (W5) has the highest results when compar

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Publication Date
Mon Aug 01 2022
Journal Name
Baghdad Science Journal
Subgroups and Orbits by Companion Matrix in Three Dimensional Projective Space
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The aim of this paper is to construct cyclic subgroups of the projective general linear group over  from the companion matrix, and then form caps of various degrees in . Geometric properties of these caps as secant distributions and index distributions are given and determined if they are complete. Also, partitioned of  into disjoint lines is discussed.

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