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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
Sat Nov 15 2025
Journal Name
Journal Of Baghdad College Of Dentistry
An Evaluation of the Efficacy of Different Gingival Retraction Materials on the Gingival Tissue Displacement (A Comparative In Vivo Study)
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Background: An accurate adaptation of the crown to the finish line is essential to minimize cement dissolution and to preserve periodontium in fixed partial denture cases. An accurate adaptation of crown is possible only when preparation details are captured adequately in the impression and transferred to cast. For these reasons, gingival displacement is necessary to capture subgingival preparation details.The aim of the present study is to measure in vivo the horizontal displacement of the gingival sulcus obtained by using three new cordless retraction materials (Magic Foam Cord®, Racegel and Astringent Retraction Paste) in comparison to medicated retraction cord. Materials and method: Thirty-two patients requiring porcelain fused to me

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Publication Date
Tue Mar 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
The effect of creating knowledge according to the model (Nonaka & Takeuchi, 1995) on organizational ambidexterity: A study on a sample of Iraqi private banks
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Purpose - This study relies on the descriptive and analytical approach through collecting and analyzing the necessary data, as this approach focuses on polling the opinions of the research sample and its directions, and aims to develop a model that studies the relationship between knowledge creation and organizational ambidexterity in Iraqi private banks and verifying its validity experimentally.

Design / Methodology / Introduction - A survey was conducted through a questionnaire form to collect data from a sample of (113) managers in private commercial banks. In addition, this study used the AMOS program and the ready-to-use statistical program package (SPSS V.25) to test the proposed hypotheses of the t

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Publication Date
Wed Jun 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
A proposed model for disclosing the role of the collective intelligence system in improving joint auditing
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This research aims to present a proposed model for disclosure and documentation when performing the audit according to the joint audit method by using the questions and principles of the collective intelligence system, which leads to improving and enhancing the efficiency of the joint audit, and thus enhancing the confidence of the parties concerned in the outputs of the audit process. As the research problem can be formulated through the following question: “Does the proposed model for disclosure of the role of the collective intelligence system contribute to improving joint auditing?”   

The proposed model is designed for the disclosure of joint auditing and the role

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Publication Date
Fri Mar 26 2021
Journal Name
Chemical Papers
DFT, anticancer, antioxidant and molecular docking investigations of some ternary Ni(II) complexes with 2‑[(E)‑[4‑(dimethylamino) phenyl]methyleneamino]phenol
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The biological activities of some ternary nickel complexes with a Schiff base obtained from 4-dimethylaminobenzaldehyde and 2-aminophenol have been reported. The Schiff base ( HL1) acts as a primary ligand whereas, anthranilic acid ( HL2), 2-nitroaniline ( HL3), alanine ( HL4) and histidine ( HL5) act as secondary ligand or co-ligand. The anticancer activity of these compounds was studied against human colon carcinoma (HCT-116), human hepatocellular liver carcinoma (HEPG-2) and human breast carcinoma (MCF-7) cell lines. As per the results, the compounds were active against the cell lines. The antioxidant activity of the same compounds was evaluated using DPPH (1,1-diphenyl-2-picryl-hydrazyl) radical scavenging and compared with ascorbic aci

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Publication Date
Mon Oct 04 2021
Journal Name
Journal Of Petroleum Exploration And Production Technology
Perforation location optimization through 1-D mechanical earth model for high-pressure deep formations
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Optimum perforation location selection is an important study to improve well production and hence in the reservoir development process, especially for unconventional high-pressure formations such as the formations under study. Reservoir geomechanics is one of the key factors to find optimal perforation location. This study aims to detect optimum perforation location by investigating the changes in geomechanical properties and wellbore stress for high-pressure formations and studying the difference in different stress type behaviors between normal and abnormal formations. The calculations are achieved by building one-dimensional mechanical earth model using the data of four deep abnormal wells located in Southern Iraqi oil fields. The magni

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Publication Date
Sun Dec 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
CALCULATION BIASES FOR COEFFICIENTS AND SCALE PARAMETER FOR LINEAR (TYPE 1) EXTREME VALUE REGRESSION MODEL FOR LARGEST VALUES
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Abstract

Characterized by the Ordinary Least Squares (OLS) on Maximum Likelihood for the greatest possible way that the exact moments are known , which means that it can be found, while the other method they are unknown, but approximations to their biases correct to 0(n-1) can be obtained by standard methods. In our research expressions for approximations to the biases of the ML estimators (the regression coefficients and scale parameter) for linear (type 1) Extreme Value Regression Model for Largest Values are presented by using the advanced approach depends on finding the first derivative, second and third.

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Publication Date
Thu Aug 31 2017
Journal Name
Journal Of Engineering
Reactive Adsorption Desulfurization by Nanocrystalline ZnO/Zeolite A Molecular Sieves
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      Nanocrystalline ZnO/Zeolite type A composite was prepared by simple method of operation by . the precipitation of zinc oxide and loading on zeolite 5A in one step. Characterization was made by X-ray diffraction (XRD), X-ray fluorescence(XRF), N2  adsorption- desorption for BET surface area, and Atomic force microscopy (AFM). Results showed that zinc oxide was loaded on zeolite as noticed by the characteristic peaks and was of nano scale having an average diameter of 88.57nm. The percentage loading of ZnO on zeolite A was 28.37% and the surface area was 222m2/g. The activity of the prepared catalyst was examined in the desulfurization of double hydrogenated diesel fuel. The process was investigated in a

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Publication Date
Sat Dec 01 2018
Journal Name
Al-khwarizmi Engineering Journal
Co-digestion of Shumblan with Different Wastes as a Source for the Biogas Production
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Shumblan (SH) is one of the most undesirable aquatic plants widespread in the irrigation channels and water bodies. This work focuses on boosting the biogas potential of shumblan by co-digesting it with other types of wastes without employing any chemical or thermal pretreatments as done in previous studies. A maximum biogas recovery of 378 ml/g VS was reached using shumblan with cow manure as inoculum in a ratio of 1:1. The methane content of the biogas was 55%. Based on volatile solid (VS) and C/N ratios, biogas productions of 518, 434, and 580 ml/g VS were obtained when the shumblan was co-digested with food wastes (SH:F), paper wastes (SH:P), and green wastes (SH:G) respectively. No significant changes of methane contents were observ

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Publication Date
Mon Aug 01 2016
Journal Name
2016 38th Annual International Conference Of The Ieee Engineering In Medicine And Biology Society (embc)
Changes in the EEG amplitude as a biomarker for early detection of Alzheimer's disease
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The rapid increase in the number of older people with Alzheimer's disease (AD) and other forms of dementia represents one of the major challenges to the health and social care systems. Early detection of AD makes it possible for patients to access appropriate services and to benefit from new treatments and therapies, as and when they become available. The onset of AD starts many years before the clinical symptoms become clear. A biomarker that can measure the brain changes in this period would be useful for early diagnosis of AD. Potentially, the electroencephalogram (EEG) can play a valuable role in early detection of AD. Damage in the brain due to AD leads to changes in the information processing activity of the brain and the EEG which ca

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Publication Date
Sun Oct 31 2021
Journal Name
International Journal Of Sustainable Development And Planning
The Crossing as a New Approach for the Urban Transformation of Traditional Cities Towards the Sustainability
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The topic of urban transformations has attracted the attention of researchers as it is one of the basic issues through which cities can be transformed towards sustainability. A specific level of transformation levels according to a philosophical concept known as a crossing. This article has relied on a specific methodology that aims to find a new approach for urban transformation based on the crossing concept. This concept derives from philosophical entrances based on the concepts of (being, process, becoming, and integration). Four levels have been for the crossing are (normal, ascending, leap, and descending). Each of these levels includes specific characteristics that distinguish it. The results showed that there is no descending

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