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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 Nov 11 2025
Journal Name
Iraqi Journal Of Science
Synthesis, Characterization and Quantum Mechanical Study of Some New 2-benzylidenehydrazinecarbothioamide Derivatives as Corrosion Inhibitors for Carbon/mild Steel in Acidic Medium.
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In this work, some of new 2-benzylidenehydrazinecarbothioamide derivatives have been prepared by condensation of thiosemicarbazide and different substituted aromatic benzaldehydes in presence of glacial acetic acid to give compounds (1-6), these compounds have characterized by its physical properties and spectroscopic methods. This work also included theoretical study to prove the ability of these compounds as corrosion inhibitors; The program package of Gaussian 09W with its graphical user interface GaussView 5.0 had used for this purpose; the methods of Density Functional Theory (DFT) with basis set of 6-311G (d,p) / hybrid function of B3LYP and semiempirical method of PM3 have been used, the study included theoretical simulation

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Publication Date
Tue Nov 11 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of olive oil as a separating medium and its effect on some physical properties of processed acrylic resin denture base (A comparative study). Part one
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Back ground: During acrylic resin processing, the mold must be separated from the surface of the gypsum to prevent liquid resin from penetrating into the gypsum, and water from the gypsum seeping into the acrylic resin. For many years, tin foil was the most acceptable separating medium, and because it's difficult to apply, a tin-foil substitute is used. In this study, olive oil is used as an alternative to tin foil separating medium for first time, so the aim of the study was to evaluate its effect as a separating medium on some physical properties such as (surface roughness, water sorption and solubility) of acrylic resins denture base comparing it with those processed using tin-foil and tin foil substitute such as (cold mold seal) separat

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Publication Date
Fri Jan 01 2021
Journal Name
Annals Of Maxillofacial Surgery
The use of screw retained hybrid arch bar for maxillomandibular fixation in the treatment of mandibular fractures: A comparative study
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Introduction: The use of screw-retained hybrid arch bars (HABs) is a relatively recent development in the treatment of mandibular fractures. The purpose of this study is to compare the clinical outcome between HAB and the conventional Erich arch bar (EAB) in the closed treatment of mandibular fractures. Materials and methods: This study included 18 patients who were treated for mandibular fractures with maxillomandibular fixation (MMF), patients were randomly assigned into a control group (n = 10) in which EAB was used and study group (n = 8) in which HAB was used. The outcome variables were time required for application and removal, gingival inflammation scores, postoperative complications, and incidence of wire-stick injury or gloves perf

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Publication Date
Wed Mar 20 2019
Journal Name
Journal Of Legal Sciences
Sale Based on an Open Price – A Comparative Study
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The ultimate goal of any sale contract is to maximize the combined returns of the parties, knowing that these returns are not realized (in long-term contracts) except in the final stages of the contract. Therefore, this requires the parties to the contract to leave some elements open, including the price, because the adoption of a fixed price and inflexible will not be appropriate to meet their desires when contracting, especially with ignorance of matters beyond their will and may affect the market conditions, and the possibility of modifying the fixed price through The elimination is very limited, especially when the parties to the contract are equally in terms of economic strength. Hence, in order to respond to market uncertainties, the

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Publication Date
Fri Dec 01 2023
Journal Name
Al-khwarizmi Engineering Journal
Development of an ANN Model for RGB Color Classification using the Dataset Extracted from a Fabricated Colorimeter
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Codes of red, green, and blue data (RGB) extracted from a lab-fabricated colorimeter device were used to build a proposed classifier with the objective of classifying colors of objects based on defined categories of fundamental colors. Primary, secondary, and tertiary colors namely red, green, orange, yellow, pink, purple, blue, brown, grey, white, and black, were employed in machine learning (ML) by applying an artificial neural network (ANN) algorithm using Python. The classifier, which was based on the ANN algorithm, required a definition of the mentioned eleven colors in the form of RGB codes in order to acquire the capability of classification. The software's capacity to forecast the color of the code that belongs to an object under de

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Publication Date
Fri Dec 01 2023
Journal Name
Al-khwarizmi Engineering Journal
Development of an ANN Model for RGB Color Classification using the Dataset Extracted from a Fabricated Colorimeter
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Codes of red, green, and blue data (RGB) extracted from a lab-fabricated colorimeter device were used to build a proposed classifier with the objective of classifying colors of objects based on defined categories of fundamental colors. Primary, secondary, and tertiary colors namely red, green, orange, yellow, pink, purple, blue, brown, grey, white, and black, were employed in machine learning (ML) by applying an artificial neural network (ANN) algorithm using Python. The classifier, which was based on the ANN algorithm, required a definition of the mentioned eleven colors in the form of RGB codes in order to acquire the capability of classification. The software's capacity to forecast the color of the code that belongs to an ob

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Publication Date
Mon Jan 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
The Word " בַּיִת " (House) in the Book of Joshua A Comparative Semitic Linguistic Study
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In this paper we have dealt with the word "  בַּיִת" in the Book of Joshua because it makes one of those that highly employed the  word    בַּיִת"  " in the Old Testament. The Book of Joshua comes  sixth   in the order of tanakh wich was written by Joshua son of  Noon in Palestine during the fifteenth century  B.C. and it covers a three-decade era extending from the death  of Moses til the death of Joshua son of Noon.

      The word " בַּיִת " in this paper refers to the place, where expressions are made by a noun modified by a noun . The modifier is"" בַּיִת , and the modified is another noun. Herein, we

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Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
IRAQ TELEVISION AND THE PROBLEM OF EMERGENCY PROGRAMS : (An Analytical Study of Emergency Programs in Iraq TV)
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The success of any media work in our contemporary life is based on proper planning. Television in Iraq is like any media outlet that adopts clear planning and programming in order to achieve the goals set in the news, entertainment, education. Iraq TV relies on four programming plans in one year (short term), but we often receive central instructions directly from the Minister of Information ordering to cancel the program plan and what was scheduled for broadcast to be finally replaced by alternative or emergency program associated with an incident, occasion or important news, these programs are all called (emergency programs).

In this present research we will be dealing with these programs as well as the extent of their impact o

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Publication Date
Mon Mar 02 2020
Journal Name
Journal Of Applied Research In Higher Education
Proposal of a guide for talent evaluation and management based on a qualitative and three-staged approach
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Purpose

The key objective of the study is to understand the best processes that are currently used in managing talent in Australian higher education (AHE) and design a quantitative measurement of talent management processes (TMPs) for the higher education (HE) sector.

Design/methodology/approach

The three qualitative multi-method studies that are commonly used in empirical studies, namely, brainstorming, focus group discussions and semi-structured individual interviews were considered. Twenty-three individuals from six Australian universities parti

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Publication Date
Thu Oct 15 2020
Journal Name
International Journal Of Energy Research
Mixed-ligand complexes of ampicillin derived Schiffbase ligand and Nicotinamide: Synthesis, physico-chemical studies, DFT calculation, antibacterial study and molecular docking analysis
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A novel series of mixed-ligand complexes of the type, [ML 1 (L 2 ) 3 ]Cl x [M = Cr(III), Fe(III), Co(II),Ni(II), Cu(II), Cd(II) and Hg(II), n = 2, 3], was synthesized using Schiffbase (HL 1 ) as main ligand, nicotinamide (L 2 ) as secondary ligand, and the corresponding metal ions in 1:3:1 molar ratio. The main ligand, HL 1 was prepared by the interaction of ampicillin drug and 4-chlorobenzophenone. The synthesized mixed ligand complexes were characterized by elemental analysis, UV-Vis, FT-IR, 1 H-NMR, 13 C-NMR and TG/DTG studies. In the mixed-ligand complexes, the Schiffbase ligand, HL 1 showed coordination to the central metal ion in tridentate manner via azomethine nitrogen, β-lactam ring oxygen and deprotonated carboxylic oxy- gen atom

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