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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 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
Fri Apr 30 2021
Journal Name
Al-kindy College Medical Journal
Slump Test versus Straight Leg Raise Test in the Diagnosing of Lumbar Disc Herniation: A Prospective Comparative Study
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Background: The clinical examination is one of the best suitable methods for diagnosis of low backache. Backache is one disease that the signs, clinical examination finding, and the results on imaging modalities not always related. The straight leg raising (SLR) and slump tests, can be used for diagnosis of lumber disc herniation.

Objectives: To compare the result of the slump test and SLR test in the diagnosis of lumber disc herniation.

Subjects and Methods: A prospective comparative study conducts on 280 patients in Al-Kindy teaching and private clinics complaints of backache, aging between 18-70 years old with acute or recurrent backache, sciatica pai

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Publication Date
Mon Jan 01 2024
Journal Name
Corporate And Business Strategy Review
The role of governance mechanisms in trust-building strategies: A comparative analytical study in public and private banks
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The study aims to build a model that enhances trust-building for public and private banks to compare and determine the significant differences between public and private banks, by testing the impact of governance mechanisms (transparency, accountability, justice, independence, and social responsibility) (Agere, 2000) on trust-building strategies (trust and trust building, people management, work relations, training and development, leadership practices, and communications) (Ngalo, 2011; Stone et al., 2005), to indicate the level of employees’ awareness of the theoretical contents of the two variables and their importance to banking work, with the aim of improving performance. The main question is the role of governance mechanisms

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Publication Date
Fri Apr 30 2021
Journal Name
Al-kindy College Medical Journal
Slump Test versus Straight Leg Raise Test in the Diagnosing of Lumbar Disc Herniation: A Prospective Comparative Study
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Background: The clinical examination is one of the best suitable methods for diagnosis of low backache. Backache is one disease that the signs, clinical examination finding, and the results on imaging modalities not always related. The straight leg raising (SLR) and slump tests, can be used for diagnosis of lumber disc herniation. Objectives: To compare the result of the slump test and SLR test in the diagnosis of lumber disc herniation. Subjects and Methods: A prospective comparative study conducts on 280 patients in Al-Kindy teaching and private clinics complaints of backache, aging between 18-70 years old with acute or recurrent backache, sciatica pain, or low back and sciatica pain for last 12 weeks, while patients

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Publication Date
Wed Feb 20 2019
Journal Name
Iraqi Journal Of Physics
Preparation of polyaniline polymer and using it as a Vapor sensor of acids
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 Polyaniline organic Semiconductor polymer was prepared by oxidation polymerization by adding hydrochloric acid concentration of 0.1M and potassium per sulfate concentration of 0.2M to 0.1M of aniline at room temperature, the polymer was deposited at glass substrate, the structural and optical properties were studies through UV-VIS, IR, XRD measurements, films have been operated as a sensor of vapor  H2SO4 and HCl  acids.

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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
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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Publication Date
Wed Jun 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
Selection of the initial value of the time series generating the first-order self-regression model in simulation modeAnd their impact on the accuracy of the model
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In this paper, compared eight methods for generating the initial value and the impact of these methods to estimate the parameter of a autoregressive model, as was the use of three of the most popular methods to estimate the model and the most commonly used by researchers MLL method, Barg method  and the least squares method and that using the method of simulation model  first order autoregressive through the design of a number of simulation experiments and the different sizes of the samples.

                  

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Publication Date
Thu Dec 15 2022
Journal Name
Bionatura
Comparative morphoanatomical study for the same rodents species in Iraq
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Samples (4th) reviewed are deposited and stored in the Iraqi Natural History Museum (INHM), and there are 4th of them. Sciurus anomalous (Güldenstädt, 1785) species are preserved and mummified. It is a Caucasian squirrel (S. anomalus) that was medium in size, with a grayish-to-chestnut color, a golden gray back, and a golden tail. It is found in the forests of East and Southeast Asia. The variety possessed for the study was previously registered in the vertebrate literature by several authors and was stored by scientific methods in the museum. As a result of the multiplication and growth of these species, and to know the environmental changes that occurred in them, they were compared with models and samples found throughout Iraq

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Publication Date
Thu Sep 13 2018
Journal Name
Baghdad Science Journal
Study of the Electric Quadrupole Moments for some Scandium Isotopes Using Shell Model Calculations with Different Interactions
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The electric quadrupole moments for some scandium isotopes (41, 43, 44, 45, 46, 47Sc) have been calculated using the shell model in the proton-neutron formalism. Excitations out of major shell model space were taken into account through a microscopic theory which is called core polarization effectives. The set of effective charges adopted in the theoretical calculations emerging about the core polarization effect. NushellX@MSU code was used to calculate one body density matrix (OBDM). The simple harmonic oscillator potential has been used to generate the single particle matrix elements. Our theoretical calculations for the quadrupole moments used the two types of effective interactions to obtain the best interaction compared with the exp

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