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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
Tue Jan 01 2019
Journal Name
Indian Journal Of Public Health Research & Development
Comparative Study of Hepcidin and Some Inflammatory Parameters in Pregnant Women at the Three Trimesters
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Publication Date
Sat Mar 01 2014
Journal Name
Journal Of The College Of Languages (jcl)
The Impact of Holy Qur’an on Pushkin’s Poetry A Comparative Study
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Praise be to Allah , the Lord of Heavens , Who revealed His Scripture in plain Arabic, and prayers and peace be upon the Master of all creatures and the chosen one , Muhammad (PBUH).Pushkin was known as a poet in Russia, the sun of its poetry that set, the father of the Russian literature and the founder of its literary language. When he published his poems, trying to express his inner poetic feelings and creative visions, he presented them with creativity and special touch. The reason behind the selection of Pushkin as the subject of this study is that he was affected by Islam and Arabs. For the purpose of this study, the dissertation has been divided into introduction and three chapters; each chapter includes two topics. In the introdu

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Publication Date
Sun Jul 04 2010
Journal Name
Journal Of Educational And Psychological Researches
Educational Curricula of preeminent and Talent:Enrichment Curriculum as a Model
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This research aimed at recognizing the properties of curricula that fitted to preeminent and talent students. Many types of these curricula were exposed, enrichment curriculum was explained as one of alternatives of available curricula.
The research used the analytical methodology for local and international literature in the field of preeminent and talent education to meet the properties of curricula that fitted to this special group of students. Many results was obtained as:
• This type of school enrichment curriculum consists of three levels( general discovery activities, individual and groups training activities, and individual or groups real problems).
• Investigation the effectively both sides of brain: right and left,

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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
A Suggested Model For Using Customer's Data Management Information System/ A Case Study In Al-Rasheed Bank/General Agent Office/ Nothren Reigon
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This study aim to  identify the concept of  web based information systems since its one of the important topics that is  usually omitted by our organizations, in addition to,  designing a web based information system in order to manage the customers data of Al- Rasheed bank, as a unified information system that is specialized to the banking deals of the customers with the bank, and providing a suggested model to apply the virtual private network as a tool that is to protect the transmitted data through the web based information system.

This study is considered important because it deals with one of the vital topics nowadays, namely: how to make it possible to use a distributed informat

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Publication Date
Tue Jun 10 2025
Journal Name
Alrafidain Of Law
The Effects of the research and technology development contract -A comparative study-
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Researching the effects of the research and technological development contract, determining its extent and demarcating the boundaries of the obligations imposed in it, is the cornerstone of economic growth and development, because defining these obligations removes the ambiguity and conflict between interests, by stating the rights owed to each party and even trying to reconcile them, or impose protection by specifying guarantees that are compatible with the essence of the R&D contract, For the purpose of studying the subject thoroughly, we will divide this research into two sections. The first is devoted to identifying the parties to the research and technological development contract. As for the other topic, we will explain the obligation

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Publication Date
Tue Oct 20 2020
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Comparison Among Three Estimation Methods to Estimate Cascade Reliability Model (2+1) Based On Inverted Exponential Distribution
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      In this paper, we are mainly concerned with estimating cascade reliability model (2+1) based on inverted exponential distribution and comparing among the estimation methods that are used . The maximum likelihood estimator and uniformly minimum variance unbiased estimators are used to get  of the strengths  and the stress ;k=1,2,3 respectively then, by using the unbiased estimators, we propose Preliminary test single stage shrinkage (PTSSS) estimator when a prior knowledge is available for the scale parameter as initial value due past experiences . The Mean Squared Error [MSE] for the proposed estimator is derived to compare among the methods. Numerical results about conduct of the considered

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Publication Date
Tue Feb 21 2017
Journal Name
Journal Of Entomology And Zoology Studies
Comparison study between a crude bacterial suspension and purified pseudomonal alkaline protease enzyme effect on the rabbit interleukin-2 bacterial keratitis
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Publication Date
Sat Jan 20 2024
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Theoretical Study of the Lasing Output for a Quasi-Three-Level Operation in Nd 3+:YAG Thin- Disk Laser
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In this research, the effect of each of the concentrations ( Nd+3) was studied (N) the thickness of the thin disk (d) the number of times that the pumping beam passes through the effective medium of this laser (Mp) the reflectivity of the laser output mirror (R 2) The losses of the effective medium (L) and the pumping power used in achieving the reverse qualification (PP) on each of the pumping threshold capacities (Pp.th) and the output power of the laser (Pout) and the efficiency (ŋ) in Nd3+ thin-disk lasers (TDLs) pumping quasi-three-level With continuous operation (cw), at room temperature, and in the Gaussian mode (TEM00),

We found under these opera

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Publication Date
Fri Jan 01 2016
Journal Name
Advances In Computing
A New Abnormality Detection Approach for T1-Weighted Magnetic Resonance Imaging Brain Slices Using Three Planes
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Generally, radiologists analyse the Magnetic Resonance Imaging (MRI) by visual inspection to detect and identify the presence of tumour or abnormal tissue in brain MR images. The huge number of such MR images makes this visual interpretation process, not only laborious and expensive but often erroneous. Furthermore, the human eye and brain sensitivity to elucidate such images gets reduced with the increase of number of cases, especially when only some slices contain information of the affected area. Therefore, an automated system for the analysis and classification of MR images is mandatory. In this paper, we propose a new method for abnormality detection from T1-Weighted MRI of human head scans using three planes, including axial plane, co

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Publication Date
Wed Aug 17 2022
Journal Name
Aip Conference Proceedings
The effect of using Gaussian, Kurtosis and LogCosh as kernels in ICA on the satellite classification accuracy
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This study focusses on the effect of using ICA transform on the classification accuracy of satellite images using the maximum likelihood classifier. The study area represents an agricultural area north of the capital Baghdad - Iraq, as it was captured by the Landsat 8 satellite on 12 January 2021, where the bands of the OLI sensor were used. A field visit was made to a variety of classes that represent the landcover of the study area and the geographical location of these classes was recorded. Gaussian, Kurtosis, and LogCosh kernels were used to perform the ICA transform of the OLI Landsat 8 image. Different training sets were made for each of the ICA and Landsat 8 images separately that used in the classification phase, and used to calcula

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