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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 Apr 30 2024
Journal Name
Iraqi Journal Of Science
Crescent Moon Visibility: A New Criterion using Deep learned Artificial Neural-Network
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     Many authors investigated the problem of the early visibility of the new crescent moon after the conjunction and proposed many criteria addressing this issue in the literature. This article presented a proposed criterion for early crescent moon sighting based on a deep-learned pattern recognizer artificial neural network (ANN) performance. Moon sight datasets were collected from various sources and used to learn the ANN. The new criterion relied on the crescent width and the arc of vision from the edge of the crescent bright limb. The result of that criterion was a control value indicating the moon's visibility condition, which separated the datasets into four regions: invisible, telescope only, probably visible, and certai

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Publication Date
Wed Sep 01 2021
Journal Name
Baghdad Science Journal
An Efficient Image Encryption Using a Dynamic, Nonlinear and Secret Diffusion Scheme
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The growing use of tele

This paper presents a new secret diffusion scheme called Round Key Permutation (RKP) based on the nonlinear, dynamic and pseudorandom permutation for encrypting images by block, since images are considered particular data because of their size and their information, which are two-dimensional nature and characterized by high redundancy and strong correlation. Firstly, the permutation table is calculated according to the master key and sub-keys. Secondly, scrambling pixels for each block to be encrypted will be done according the permutation table. Thereafter the AES encryption algorithm is used in the proposed cryptosystem by replacing the linear permutation of ShiftRows step with the nonlinear and secret pe

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Publication Date
Fri Jan 01 2021
Journal Name
Computers, Materials & Continua
A New Hybrid Feature Selection Method Using T-test and Fitness Function
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Publication Date
Sun Jan 30 2022
Journal Name
Iraqi Journal Of Science
A Survey on Arabic Text Classification Using Deep and Machine Learning Algorithms
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    Text categorization refers to the process of grouping text or documents into classes or categories according to their content. Text categorization process consists of three phases which are: preprocessing, feature extraction and classification. In comparison to the English language, just few studies have been done to categorize and classify the Arabic language. For a variety of applications, such as text classification and clustering, Arabic text representation is a difficult task because Arabic language is noted for its richness, diversity, and complicated morphology. This paper presents a comprehensive analysis and a comparison for researchers in the last five years based on the dataset, year, algorithms and the accuracy th

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Publication Date
Thu Feb 01 2018
Journal Name
Iet Signal Processing
Signal compression and enhancement using a new orthogonal‐polynomial‐based discrete transform
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Publication Date
Thu Apr 24 2025
Journal Name
Pertanika Journal Of Science And Technology
Enhancing Leachate Treatment with Electrocoagulation: A Computational Approach Using Response Surface Methodology
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Malaysia's growing population and industrialisation have increased solid waste accumulation in landfills, leading to a rise in leachate production. Leachate, a highly contaminated liquid from landfills, poses environmental risks and affects water quality. Conventional leachate treatments are costly and time-consuming due to the need for additional chemicals. Therefore, the Electrocoagulation process could be used as an alternative method. Electrocoagulation is an electrochemical method of treating water by eliminating impurities by applying an electric current. In the present study, the optimisation of contaminant removal was investigated using Response Surface Methodology. Three parameters were considered for optimisation: the curr

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Publication Date
Tue Dec 27 2022
Journal Name
Chemical Papers
Synthesis, characterization, and application of external gelation of sodium alginate nanoparticles in molecular imprinting for separation and drug delivery of tenoxicam
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Publication Date
Sun Oct 09 2022
Journal Name
Journal Of Research In Medical And Dental Science
Efficacy of Locally Applied K-Carrageenan on the Healing of Thermal Burn in Rat-Experimental Model: Histological Study
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ABSTRACT Wound is damage or disruption to the normal anatomical structure and function. Carrageenan is sulphated polysaccharide found in Gigartina, Chondrus and Eucheuma species in the red algal family. Having anticancer, anti-inflammatory and renewal of tissues. Our study aimed to detect the role of kappa carrageenan in the burned skin wound repair. Skin burn were performed in the right and left cheek of 20 male rats (aged 7-8 weeks weighing 300-350 g). Burned skin rats were categorized into two equal groups. Burned areas of right side were treated with a local application of 1 ml of kappa carrageenan solution once daily (treatment group) and the left side receive no treatment (control group). After 5, and 10 days, 5 rats from each

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Publication Date
Sat Feb 09 2019
Journal Name
Journal Of The College Of Education For Women
The martial rights and duties (Rights and duties of a woman and a man)
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This research addresses the relevance of men and women and the consequent provisions
such as dowry and alimony ... Of the like, marriage is to organize links masculinity and
femininity any sexual meeting between men and women a special system that must be
produces reproduction him and alone, which gets its reproduction in human kind, and has no
family and on the basis of private life is being organized.
The importance of the topic see Islam has urged marriage and forbade celibacy, and ensure
that the Lord of Glory Almighty married subsidy nor the origin of the differences between
men and women in money or workmanship or blue-chip Every Muslim inept any Muslim and
every Muslim efficient for any Muslim.
The impor

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Publication Date
Fri Jan 01 2021
Journal Name
Bionatura
STUDY THE TIGRIS RIVER IN SOUTH OF BAGHDAD CITY AND MAY USE IT AS IRRIGATION WATER
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