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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
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
Solar ray tracing programs to find new types of solar
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Anew Solar concentrator have been designed in this paper, this concentrators Were based on the total internal reflection in a prism, the prism angles has been calculated by depending on the solar incident ray angle in baghdad for a year. The optical design consist ofa triangular presume, Where the solar cells on one side of the prism Wh?le the prism head towered the south. The results show that there is an increasing in the solar ray concentrators and the cell area is reduced.

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Publication Date
Mon Jan 02 2017
Journal Name
Al-academy
The use of Puppets in the educational process of Scientific topics, Like physics " Archimedes Principle as a typical example "
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This Study presents and provides Variable thoughts and aspects for representing Scientific topics " Physics for instance " as Play Shows for high School Students, by Showing a suggested Method that will Contribute in illustrating the Steps of writing the educational Scientific topic, and this method will help teachers to deliver their message to the Students " receivers " easily.The researcher have used Puppets in this method as the assisting tool for teachers, to help them deliver message Clearlym easily and Joyful.The researcher in his experiment used " Archimedes Principle " as a typical example, by Converting it into a theatrical Script, with respect to the Concept of Science, and in accordance to the Scientific educational Curriculu

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Publication Date
Sat Aug 21 2021
Journal Name
مجلة الدراسات المستدامة
A Linguistic Study of Comment Clauses in the American Series “Friends “
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The present study is a linguistic study of comment clauses in the American Series „Friends‟ .Comment clauses refer to those clauses which comment on the content of the main clause or the attitude of the speaker towards the way of speaking .The problem of this study is to answer the following questions ; what types of comment clauses can be used in the face- to –face conversations , for what functions these comment clauses could be used , and how these comment clauses are used by the participants of these conversations . This study is a qualitative one . The study aims to investigate the types of comment clauses used in the American Series “Friends‟. The study also aims to investigate the pragmatic functions of these comment clause

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Publication Date
Tue Mar 30 2010
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Numerical study of the mixed convection flow over a square cylinder
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In this work, a numerical study is performed to predict the solution of two – dimensional, steady and laminar mixed convection flow over a square cylinder placed symmetrically in a vertical parallel plate. A finite difference method is employed to solve the governing differential equations, continuity, momentum, and energy equation balances. The solution is obtained for stream function, vorticity and temperature as dependent variables by iterative technique known as successive over relaxation. The flow and temperature patterns are obtained for Reynolds number and Grashof number at (Re= -50,50,100,-100) (positive or negative value refers to aidding or opposing buoyancy , +1 assisting flow, -1 opposing flow) and (102 to 105) , respective

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Publication Date
Tue Jun 30 2015
Journal Name
College Of Islamic Sciences
The formula is effective in Surat Nisa: (A study of gramophone)
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The formula is effective in Surat Nisa
(A study of gramophone)

in the name of o Allah the Merciful
Praise be to Allah, Lord of the Worlds, and prayers and peace be upon the Seal of the Prophets and Messengers. The envoy is a mercy to the worlds Muhammad Sadiq Al - Amin and to the pure and good companions of the Tayyibites.
The formula of the morphological formulas, which have diverged from other meanings, whether lexicon or contextual and what this formula contains many meanings (effective source) and (effective in the sense of effective) and (effective sense reactor) and (effective sense) and ( (F) in the sense of a similar character) and ((the name of the) (collect). This was dealt with in the formula in Surat al-Nisaa

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Publication Date
Sun Sep 30 2007
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Study in to the Dynamic Behavior of Packed Distillation Column
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The study of the dynamic behavior of packed distillation column was studied by frequency response analysis using Matlab program. A packed distillation column (80 mm diameter) (2000 mm height) filled with glass packing (Raschig Rings 10mm), packing height (1500 mm) has been modified for separation of methanol-water mixture (60 vol%). The column dynamic behavior was studied experimentally under different step changes in, feed rate (±30%), reflux rate (±22%), and reboiler heat duty (±150%), the top and bottom concentration of methanol were measured. A frequency response analysis for the above step response was carried out using Bode diagram, the log modulus and the phase angle were  used to analyze the process model. A Matlab progra

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Publication Date
Sun Sep 06 2015
Journal Name
Baghdad Science Journal
A study of the effect of new cobalt (II) complex and cyclophosphamide drug on (GPT, ALP) activity by using in vivo system
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The present work involved a study the effect of cobalt(II) complex with formula [CoL(H2O)NO3] .4ETOH where L=Nitro [5-(P-nitro phenyl) -4-phenyl-1,2,4 traizole-3-dithiocarbamato hydrazide] aqua. (4) Ethanol and anti-cancer drug - cyclophosphamide on specific activity of two liver enzymes (GPT,ALP) by utilizing an in vivo system in female mice. On the enzymatic level an inhibition in the activity of GPT was noticed in different body organs such as liver, kidney and lung. The inhibition was noticed in both test and cyclophosphamide drug (cp). Mice were treated with three doses of cyclophosphamide (90,180, 250) ?g/ mouse for three days. The same doses were used for the cobalt (II) complex. The liver shows the highest rate of(GPT) inhibition co

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Publication Date
Mon Mar 01 2010
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The dropping of three zeroes from Iraqi dinar
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           The purpose of this research is to explain the effect of the dropping of three zeroes from Iraqi dinar on the basic role of the dinar and derivative and dynamic in transaction of Iraqi economic. the importance of this research comes from the effect of this operation on the evaluation of the exchange between the individuals of Iraqi society and the other between the Iraqi individuals and the foreign whom use the Iraqi dinar as a tool for exchange also the effect of the operation on the reserves of the Iraqi dinar the results of this research are as the following:-

1-the operation of dropping of zeroes must be associated with increase of the sharing of economic sectors wi

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Publication Date
Tue Mar 10 2020
Journal Name
Journal Of Research On The Lepidoptera
Study of the Association of Glucagon like Peptide-1 Receptors (GLP-1R) Gene Polymorphism and GLP-1 Hormone Levels in Type 2 Diabetics Patients in Iraq
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Publication Date
Wed Aug 13 2014
Journal Name
Journal Of Biotechnology Research Center
In Vivo Study for Measuring the Toxicity of Heat Stable Enterotoxin (a) Produced by Enterotoxigenic Escherichia coli in Mice
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This research was conducted to measure the safety of heat stable enterotoxin a (STa) produced by enterotoxigenic Escherichia coli, through studying its toxic effect on mice since it showed a promising effect in reducing the proliferation of colorectal cancer cells. The cytogenetic effect was determined after giving five different doses (100, 200, 400, 800 and 1600)μg/Kg in comparison with negative (phosphate buffer saline / PBS) and positive (mitomycin C/ MMC, at doses of 2 and 5μg/Kg) controls on mouse bone marrow cells by employing the following parameters: mitotic index, chromosomal aberrations and micronucleus, also, the serum level of liver functional enzymes (GOT, GPT, ALP) was recorded. In addition, lethal dose 50 (LD 50) with cert

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