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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 Jun 01 2007
Journal Name
Journal Of The College Of Languages (jcl)
TECHNIQES OF SURREALISM: A STUDY IN TWO NOVELS BY THOMAS PYNCHON, V. AND THE CRYING OF LOT 49
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Surrealism is a twentieth-century literary and artistic movement oriented toward the liberation of the mind. Surrealism is a reaction to the philosophy of rationalism which was believed to be the cause of the disaster of World War I. It emphasizes the expression of the imagination as revealed in dreams and presented without conscious control, the unexpected juxtapositions of objects, the withdrawal of the self, and the exploitation of chance effects.
Surrealism began in Paris in the early 1920s, as Europe emerged from the devastation of World War I. A group of writers, artists, and filmmakers, led by the poet André Breton, adopted the word surréaliste (meaning, roughly, "super-real") as a label for their artistic activities. Influen

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Publication Date
Fri Dec 31 2021
Journal Name
Review Of International Geographical Education
Investing Organizational Identity in Improving Work Teams: An Exploratory Study of a Sample of The Capital's Traffic Directorates
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The research aims to identify the role of organizational identity in improving work teams, and to suggest ways to deal with the outputs of work teams in a way that achieves the goals of the Baghdad Traffic Directorate as it is the subject of the application of the research, while the research community was represented by its officers, while the research sample was embodied in (General Director, Associate The Director General, the directors of Rusafa and Karkh traffic and their assistants, as well as the heads of the divisions and the officials of the departments) in it. The sample was (200) observations. The descriptive exploratory approach was devoted to conducting the research, relying on the questionnaire in data collection, as well as e

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Publication Date
Fri Mar 31 2017
Journal Name
Al-khwarizmi Engineering Journal
Experimental Study to the Effect of Natural Particles Added to Unsaturated Polyester Resin of a Polymer Matrix Composite
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Experimental investigations had been done in this study to demonstrate the effect of natural particles used as a reinforcement material to unsaturated polyester resin. The tensile test and water absorption were investigated according to (ASTM D638) and (ASTM D570), respectively. The influence of sunflower husk and pomegranate husk particles, used as a reinforcement material, on the tensile strength, Young's modulus and water absorption with different weight fraction (3%, 7% and 10%) and particle grain size (50µm, 100 µm and 150 µm), has been investigated. The water absorption of polymer composites was studied by measuring the specimen weight before and after immersion in water for one hundred days. In the experiments of tensile test,

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Publication Date
Mon Sep 30 2019
Journal Name
College Of Islamic Sciences
Detailed interpretation of Sheikh Abdullah Knon A look at the curriculum and method of innovation Critical inductive study
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The problem lies in the main research Where the site of this interpretation of the books of interpretation and what is new and how?
The objectives of this research Vjat to give a quick overview of Sheikh Kenon and the qualifications that made him interpreter, as the goal of the research to reveal the method of Sheikh Kenon highlighting what he has and what is new and show.
The researcher used the inductive method to read the whole book and the comparative approach to compare it with others. He also used the critical method to distinguish between the positions of strength and weakness in the book. The most important results are as follows: :
1 - Sheikh Abdullah Kenon language writer familiar with many sciences, such as jurisprude

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Publication Date
Tue Apr 04 2023
Journal Name
International Journal Of Professional Business Review
Risk Premium, Interest Rate, Inflation and FDI in the Time of Coronavirus: a Case Study of Mena Countries
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Purpose:  the purpose of study is estimate the Risk premium, Interest rate, Inflation and FDI in the through of Coronavirus in the MENA countries.   Theoretical framework: The theoretical framework included the study of the main variables, which are risk premium, interest rate, inflation, and foreign direct investment during the Corona virus pandemic.   Design/methodology/approach:  Concentrating on “COVID-19”, as an effective factor on the Foreign direct investment (FDI), I employ data of “MENA (Middle East and Northern Africa)” countries from 2000 to 2021 to investigate the impact of COVID-19, financial and macroeconomic indicators on FDI relying on the analytic research approach of Static panel data regression, includ

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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
Qualification Of Human Resources To Apply Electronic Management A case study In The Ministry Of Science And Technology
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     This research aims to shed light on the reality of the process of rehabilitation of human resources for the implementation of electronic management practice in the ministry, and availability requirements of the application of electronic management and diagnosis of the most important stages and steps that can be followed in the process of transition towards electronic management to keep abreast of developments in the field of information technology, has been the application of this research in the Ministry of science and technology on a group of heads of departments and directors of the people in the departments of the Ministry through the use of case study method, which includes cohabitation field intervi

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Publication Date
Mon Mar 09 2015
Journal Name
Monthly Notices Of The Royal Astronomical Society
A reliable iterative method for solving Volterra integro-differential equations and some applications for the Lane–Emden equations of the first kind
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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
The Direct Gene Injection Using of Egg Yolk Emulsion as Carrier and its Comparison with Liposomes.
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The efficiency of egg yolk emulsion in coating DNA and its delivery across cellular membranes was evaluated in comparison with liposomes DOPE . The murine leukemia viral oncogene v-abl , cloned on pBR322 was used as a DNA substrate for direct injection into mice tissue . the DNA complexes were prepared by mixing the DNA with egg yolk emulsion and liposome . Each was directly injected into mice peritoneal cavity with proper control. The gene delivery was examined phenotypically by blood analysis and cytogenetic analysis . Chromosomal changes were detected in the bone marrow as from the fourth day post inoculation through the eleventh day when chromosomal ring s could be seen . this was accompanied by decrease in the WBC count ,

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Publication Date
Thu Oct 01 2015
Journal Name
Journal Of Engineering
Studying the Utility of Using Reed and Sawdust as Waste Materials to Produce Cementitious Building Units
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In this research, the possibility of using waste wooden materials (reed and sawdust) was studied to produce sustainable and thermal insulation lightweight building units , which has economic and environmental advantages. This study is intended to produce light weight building units with low thermal conductivity, so it can be used as partitions to improve the thermal insulation in buildings. Waste wooden materials were used as a partial replacement of natural sand, in different percentages (10, 20, 30, and 40) % . The mix proportions were (1:2.5) (cement: fine aggregate) with w/c of 0.4. The values of 28 days oven dry density ranged between (2060-1693) kg/m3.The thermal conductivity decreased from (0.745 to 0.2

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Publication Date
Wed Sep 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
The Usefulness of Mandibular Ramus as an Indicator in Sex Differentiation Using 3D Reconstructed Computed Tomography
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Background: Determination of sex from an unknown human bone is an important role in forensic and anthropology field. The mandible is the largest and hardest facial bone, that commonly resist postmortem damage and forms an important source of information about sexual dimorphism. Mandibular ramus can be used to differentiate between sexes and it also expresses strong univariate sexual dimorphism. This study was undertaken to assess the usefulness of mandibular ramus as an aid in sex differentiation using CT scanning among Iraqi population. Materials and methods: 3D reconstructed computed tomography scanning of 140 Iraqi Arab subjects, (7 0 males and 70 females) were analyzed with their age range from 20-60 years old. The linear measurements w

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