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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
Thu Jun 20 2019
Journal Name
Baghdad Science Journal
Teen-Computer Interaction: Building a Conceptual Model with Thoughts- Emotion-Behaviour
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Teen-Computer Interaction (TeenCI) stands in an infant phase and emerging in positive path. Compared to Human-Computer Interaction (generally dedicated to adult) and Child-Computer Interaction, TeenCI gets less interest in terms of research efforts and publications. This has revealed extensive prospects for researchers to explore and contribute in the region of computer design and evaluation for teen, in specific. As a subclass of HCI and a complementary for CCI, TeenCI that tolerates teen group, should be taken significant concern in the sense of its context, nature, development, characteristics and architecture. This paper tends to discover teen’s emotion contribution as the first attempt towards building a conceptual model for TeenC

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Publication Date
Thu Jan 01 2015
Journal Name
Journal Of Toxicology
Acute β - N -Methylamino-L-alanine Toxicity in a Mouse Model
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The cyanobacterial neurotoxinβ-N-methylamino-L-alanine (BMAA) is considered to be an “excitotoxin,” and its suggested mechanism of action is killing neurons. Long-term exposure to L-BMAA is believed to lead to neurodegenerative diseases including Parkinson’s and Alzheimer’s diseases and amyotrophic lateral sclerosis (Lou Gehrig’s disease). Objectives of this study were to determine the presumptive median lethal dose (LD50), the Lowest-Observed-Adverse-Effect Level (LOAEL), and histopathologic lesions caused by the naturally occurring BMAA isomer, L-BMAA, in mice. Seventy NIH Swiss Outbred mice (35 male and 35 female) were used. Treatment group mice

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Publication Date
Tue Mar 01 2016
Journal Name
Journal Of Engineering
A reformation Study about the Construction Management in the Primary Stage Curricula’s for the Civil Engineering in Some of the Iraqi Universities
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There is no doubt that the field of education and teaching (in any country and whatever its ruling system varies “d”) is considered one of the most specific and sensitive field, because it is related to the building of human. And as the human is a purpose (aim) and the means in the same time and he is the strategist capital, so he way of his rearing, education, choosing the educator, methods of working and the aims are considered serious matters.

     The educational process has aim determined by the society for him self through its working establishments in this field and these are the official and public establishments. And as he feels that the establishments have failed to achieve its d

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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
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
Mon Feb 22 2021
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
MRI images series segmentation using the geodesic deformable model
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Publication Date
Wed Jan 01 2014
Journal Name
International Journal Of Computer Applications
Mobile Position Estimation based on Three Angles of Arrival using an Interpolative Neural Network
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In this paper, the memorization capability of a multilayer interpolative neural network is exploited to estimate a mobile position based on three angles of arrival. The neural network is trained with ideal angles-position patterns distributed uniformly throughout the region. This approach is compared with two other analytical methods, the average-position method which relies on finding the average position of the vertices of the uncertainty triangular region and the optimal position method which relies on finding the nearest ideal angles-position pattern to the measured angles. Simulation results based on estimations of the mobile position of particles moving along a nonlinear path show that the interpolative neural network approach outperf

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Publication Date
Fri Nov 21 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Force decay of orthodontic elastomeric chains by using three different mechanisms simulating canine retraction
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Background: The ideal force-delivery system must: provide optimal tooth moving forces that elicit the desired effects, be comfortable and hygienic for the patient, require minimal operator manipulation and patient cooperation and provide rapid tooth movement with minimal mobility during orthodontic therapy, the elastomeric chains have the greatest potential to fulfill these requirements. Materials and Methods: This in vitro study was designed to determine the effect of three different mechanisms for canine retraction : (6-3 , 6-5-3 and chain loop ) on the load relaxation behavior of three types of elastomeric chains : (maximum clear , maximum silver and extreme silver) from the same company (Ortho Technology company) with two different bran

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Publication Date
Thu Jan 05 2012
Journal Name
مجلة كلية التربية الأساسية/ جامعة بابل / بحوث المؤتمر العلمي الرابع لكلية التربية الأساسية/جامعة بابل 2011 م
THE DYNAMIC EVOLUTION OF THE SHELL NEBULAE BY USING INTERACTING WIND MODEL
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Publication Date
Sat Feb 02 2019
Journal Name
Journal Of The College Of Education For Women
Semantic features in the phenomena in the pottery of Dr. Ahmed Sulaiman Al-Ahmed / Trees behind fence as a sample: Semantic features in the phenomena in the pottery of Dr. Ahmed Sulaiman Al-Ahmed / Trees behind fence as a sample
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Abstract
This research deals with studying and analysis of a poetic group under the
title (Trees behind fence) of the great poet Dr. Ahmed Sulaiman AlAhmed
who is the some of the Shek , Sulaiman Al-Ahmed who is the linguist - poet
and famous jurist member in the Arabic scientific assemble in Damascus and
brother of the great poet Badawi Al-Jabal. This poetic group include two big
poetic legends : the first one is (Trees behind fence , ) which include one
hundred and eighty four line and the second one ( AZ-Mebadia ) which is
consists of one hundred and seventy eight line, both of them from the (Al-
Camil ) meter which is free rhyme which bears a many meaning and pictures
and just the great poet composite the

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