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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
Fri Jan 23 2026
Journal Name
Al–bahith Al–a'alami
Graduate Media Students’ Satisfaction Level in Their Program of Study:  The level of Satisfaction about the Study Programs of the masters of Media students / Case Study of Media faculties’ students at “Yarmouk University,
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The current study is considered a field study to measure the level of satisfaction of the academic programs of Media Masters students. That was accomplished through surveying the attitudes of the students who are enrolled in the faculties of media at the following universities: (Petra University, The Middle East University (MEU), and Al-Yarmouk University). Those students were enrolled in the master’s program within the formal educational system during the second semester of the academic year (2015 – 2016). This survey aims to identify the services, facilities and academic programs provided by the concerned faculties. It, also, aims to identify the public relations, administrative, educational and services aspects of those faculties.

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Publication Date
Wed Jan 01 2025
Journal Name
Socar Proceedings
Enhanced permeability estimation in non-cored wells using a modified flow zone index-permeability crossplot: a case study of carbonate reservoirs
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The permeability estimates for the uncored wells and a porosity function adopting a modified flow zone index-permeability crossplot are given in this work. The issues with implementing that approach were mostly crossplots, due to the influence of geological heterogeneity, did not show a clear connection (scatter data). Carbonate reservoir flow units may now be identified and characterized using a new approach, which has been formally confirmed. Due to the comparable distribution and flow of clastic and carbonate rock fluids, this zoning method is most effective for reservoirs with significant primary and secondary porosity. The equations and correlations here are more generalizable since they connect these variables by combining cor

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Publication Date
Mon Sep 03 2018
Journal Name
Al-academy
The Aesthetic Preoccupations of the Implicit Pattern in the Discourse of the Theatre Show (Revelations Play) - A Model
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The implicit pattern is one of the cultural patterns that are present in both the text and theatrical presentation and the reading of the implicit pattern cannot take place without cognitive references, whether audio or visual as well as historical references and the natural, social and psychological dimensions of communities and individuals.

         The researcher, in this study, attempted to focus on the axis of the aesthetic preoccupations of the implicit pattern in the theatrical presentation and the definition of the implicit pattern. Methodologically speaking, the research problem focused on revealing the outlines and the main features in the aesthetic preoccupations that shape the i

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Publication Date
Sun Dec 31 2023
Journal Name
College Of Islamic Sciences
Imam Al-Mubarakpuri's Jurisprudential Choices (d.1353 AH) in the Borders from his book "Tuhfat Al-Ahwadi" with the explanation of "Jami' Al-Tirmidhi / a comparative jurisprudential study
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Praise be to God, Lord of the Worlds, and prayers and peace be upon the Master of Messengers and his family and companions.

The study of the jurisprudential opinions of scholars, their choices, or their weightings, sheds light on the approach they followed in their choices, and reveals the originality of the scholar or his influence on those who preceded him from among the scholars.

And the commentators of the noble hadith of the Prophet have their important contributions in this aspect, as they undertake the task of explaining the noble hadith, the second source of legislation

Contemporary commentators have their share in the service of the honorable hadith, and the statement of their choices and preferences, and am

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Publication Date
Fri Jul 01 2016
Journal Name
Journal Of Engineering
Determination of Mono-crystalline Silicon Photovoltaic Module Parameters Using Three Different Methods
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For modeling a photovoltaic module, it is necessary to calculate the basic parameters which control the current-voltage characteristic curves, that is not provided by the manufacturer. Generally, for mono crystalline silicon module, the shunt resistance is generally high, and it is neglected in this model. In this study, three methods are presented for four parameters model. Explicit simplified method based on an analytical solution, slope method based on manufacturer data, and iterative method based on a numerical resolution. The results obtained for these methods were compared with experimental measured data. The iterative method was more accurate than the other two methods but more complexity. The average deviation of

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Publication Date
Thu Dec 01 2022
Journal Name
Environmental Nanotechnology, Monitoring & Management
Synthesis of nano-magnetite and magnetite/synthetic geopolymer nano-porous composite for application as a novel adsorbent
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In this work magnetite/geopolymer composite (MGP) were synthesized using a chemical co-precipitation technique. The synthesized materials were characterized using several techniques such as: “X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), vibrating sample-magnetometer (VSM), field-emission scanning electron microscopy (FE-SEM), energy dispersive X-ray spectroscopy (EDS), Brunauer–Emmett–Teller (BET) and Barrentt-Joyner-Halenda (BJH)” to determine the structure and morphology of the obtained material. The analysis indicated that metal oxide predominantly appeared at the shape of the spinel structure of magnetite, and that the presence of nano-magnetite had a substantial impact on the surface area and pore st

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Publication Date
Wed Feb 20 2019
Journal Name
Political Sciences Journal
Independent government agencies in Iraq / Integrity Commission a model
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The state did not witness the emergence of independent bodies because of the nature of the ruling regimes that were characterized by political tyranny represented by the king at the time, as is the case with Greece and the Greeks and Persia and the Romans and others. As for the Islamic state, which emerged later, it saw the emergence of what looks like independent bodies that we see today, There was the so-called Diwan Al-Hesba and the Ombudsman's Office as an independent body from the Islamic State, which operated independently to support the oppressed and the equitable distribution of financial resources, even though it was headed by well-known governors of justice and honesty. A state in the modern era, many countries, especially in E

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Publication Date
Wed Sep 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of Systemic C-reactive Protein as a Systemic Inflammatory Marker in the Blood for Patients Undergoing Minor Oral Surgical Procedures
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Background: C-reactive protein (CRP) is an acute phase protein that its plasma levels increase after trauma or surgery so it is used as an indicator for the level of inflammation after surgery. The objective of this study is to investigate pre- and post-operative levels of CRP in three types of oral surgical interventions (Apicoectomy, Impaction, and Impacted teeth exposure). Materials and Methods: A total number of (48) healthy individuals aged (20-60) years who needed oral surgical intervention for either (removal of impacted third molars, exposure of an impacted canine, or Apicoectomy). A 4ml venous blood was obtained from each patient at two occasions (pre-operatively at the day of operation and post-operatively after 48 hours), then ce

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Publication Date
Tue Mar 26 2024
Journal Name
Scientific Reports
An in vitro assessment of the residual dentin after using three minimally invasive caries removal techniques
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Abstract<p>To evaluate the efficiency and effectiveness of three minimally invasive (MI) techniques in removing deep dentin carious lesions. Forty extracted carious molars were treated by conventional rotary excavation (control), chemomechanical caries removal agent (Brix 3000), ultrasonic abrasion (WOODPECKER, GUILIN, China); and Er, Cr: YSGG laser ablation (BIOLASE San Clemente, CA, USA). The assessments include; the excavation time, DIAGNOdent pen, Raman spectroscopy, Vickers microhardness, and scanning electron microscope combined with energy dispersive X-ray spectroscopy (SEM–EDX). The rotary method recorded the shortest excavation time (p < 0.001), Brix 3000 gel was the slowest. DIAGNOdent pen va</p> ... Show More
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Publication Date
Mon Aug 04 2014
Journal Name
Iraqi National Journal Of Chemistry
Comparative Study for Antibacterial Activity of Some Maleamic acid Derivatives with Some Commercial Antibiotic
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