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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
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Account the expected values ??for a single particle to a group of atoms and ions
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Technique was used to retail for analyzing atom beryllium ion cathode of an atom lithium to six pairs of functions wave which two ?????? and the rest of the casing moderation and to analyze atom lithium ion Mob atom beryllium to three pairs of functions wave pair of casing and the rest of the casing moderation using function wave Hartree Fock and each casing email wascalculate expected values ??....

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Publication Date
Fri Jul 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Using system dynamics model and the statistical indicators for Road Map of "Green government departments" project In Iraq
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Abstract                                                         

The issue of the protection of the environment is a shared responsibility between several destinations and sectors, and constitutes a main subject in which they can achieve sustainable development. In the sectors of government programs can be set up towards the establishment of the government sector to the green environment, so to be the implementati

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Publication Date
Sat Dec 15 2018
Journal Name
Journal Of Baghdad College Of Dentistry
The accuracy of ridge mapping procedure in determining the alveolar ridge width
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Background: Post-extraction alveolar ridge resorption is unavoidable phenomenon ending with insufficient ridge width. Measuring the physical dimensions of the available bone before implant surgery is an important aspect of diagnosis and treatment planning. Bone height can be calculated from radiographs, while bucco-lingual ridge width can be measured by conventional tomography, CT scanning and ridge mapping.

Radiographic techniques have certain disadvantages. Therefore the ridge mapping technique was used as an option for determining alveolar ridge width.

The purpose of this study was to compare the validity of alveolar ridge width measurements obtained with ridge mapping technique before surgical flap reflection against

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Publication Date
Sun Dec 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
The Determinants of Total Factor Productivity Growth: an Analytical Study of a Cross Section of Countries for the Period (2003-2016)
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            This study tests the effect of a large number of independent variables that control the growth of the total productivity, which amounted to 112 variables, gathered from what is mentioned in the specialized theoretical and applied literature. The data for these variables were taken from global reports of sound international organizations and reliable databases covering the period 1991-2016. The data of the dependent variable, the growth of the total factor productivity, were taken from the database of the world development indicators. The study covered 61 countries for which data were available. The study included three regression models to explain

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Publication Date
Wed Dec 11 2019
Journal Name
Journal Of The College Of Education For Women
Alternatives Scenarios for Transportation During The Morning and Evening Peaks (The Entrances of The Jadiriya Complex Study Case) "A Planning Vision"
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The research aims to develop alternatives to transportation at the entrance to the Educational City (University of Baghdad) during the morning and evening peaks, which result from of the traffic congestion at the entrances to the educational city (the University of Baghdad), and affects the emotional, functional, and social performance of the whole city, and leads to hotbeds of confluence and congestion at the entrances in the morning and evening peaks. This movement was measured on the ground for pedestrians and vehicles. Some criteria were adopted to determine the density of road length to the area and density of roads for the number of users and the rate of the area served by roads. The research reviews the experiences of some

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Publication Date
Wed Jan 30 2019
Journal Name
Modern Sport
Evaluation of training programs according to some physical abilities, functional indicators and achievement for men's 200m runners
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The effectiveness of (200 m) of the events of extreme intensity and this is characterized by training in the anaerobic energy system prevailing in the result of this privacy as these are based on the physical abilities and functional indicators identified in this direction and hence the importance of research in the evaluation of training programs on the basis of physical abilities and some indicators of the functionality of the hostile 200 m . The study aimed to: 1. Evaluation of training programs according to physical abilities and some functional indicators of hostile men.The researchers used the descriptive analytical method to suit the nature of the research. The researchers selected them research sample by the deliberate method of the

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Publication Date
Tue Oct 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
The impact of the RMB exchange rate on the value of Chinese exports For the period (1978-2017) using the Angel-Granger model
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In this research, we sought to identify the nature of the relationship between the exchange rate of the Chinese yuan and the value of Chinese exports, through the formulation of a standard model based on the model of common integration, and based on the data of the study and using the test "Angel-Granger" It reflects the relationship between the two research variables, through which the relationship between the RMB exchange rate and the value of Chinese exports was estimated during the period 1978-2017.

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Publication Date
Tue Jan 01 2019
Journal Name
The Turkish Journal Of Endocrinology And Metabolism
Cell-free DNA as a Clinical Indicator in Maternal Blood
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As many expensive and invasive procedures are used for the diagnosis or follow-up of clinical conditions, the measurement of cell-free DNA is a promising, noninvasive method, which considers using blood, follicular fluid, or seminal fluid. This method is used to determine chromosomal abnormalities, genetic disorders, and indicators of some diseases such as polycystic ovary syndrome, pre-eclampsia, and some malignancies. Cell-free DNA, which are DNA fragments outside the nucleus, originates from an apoptotic process. However, to be used as a marker for the previously mentioned diseases is still under investigation. We discuss some aspects of using cell-free DNA measurements as an indicator or marker for pathological conditions.

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Publication Date
Sun Jan 01 2023
Journal Name
International Conference On Scientific Research & Innovation (icsri 2022)
Saccharomyces Cerevisiae as a human pathogen in renal transplant recipients
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Publication Date
Sat Dec 01 2018
Journal Name
Political Sciences Journal
political culture as a tool to analyse Decentralization Experience in
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It sheds light on the cultural dimension in the decentralized administration experience in Iraq as evaluation tool by adding a new dimension in studying decentralization in addition to the administrative, political and legal dimensions .The proposal of study is that without the civil political culture ,the administrative decentralization in Iraq which remains weak and it may be imposed to a set of problems. - The study includes an introduction, conclusion and a set of political and cultural issues , its components and it may have the political analysis of this culture and its role in determining the movement of the administrative decentralized movement in Iraq post 2003.

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