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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 Jun 26 2023
Journal Name
Journal Of Contemporary Medical Sciences
Glyceryl Trinitrate, a Vasodilating Drug Acts as an Antibiofilm Agent in Serratia marcescens
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Objectives: Serratia marcescens is a gram-negative pathogen of many species. The ability of S. marcescens to form biofilms and its potent innate resistance to antimicrobials and cleaning solutions are both essential for its pathogenicity and survival. The present study was conducted to investigate the effect of glyceryl trinitrate (GTN) on the biofilm of S. marcescens, as an alternative for antibiotic therapy. Methods: Different specimens, including ear swabs, burns, mid-stream urine, wound swabs, and sputum, were collected from patients who were brought to Al-Ramadi Hospital, Iraq. All samples were cultured, and the colonies that were obtained were detected using the VITEK® 2 compact. The ability of biofilms to develop was e

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Publication Date
Sat Dec 28 2024
Journal Name
Journal Of Physical Education
The Effect of the (Team - Pair - Solo) Strategy in Learning the Accuracy of the Spiking Skill in Volleyball
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This study aims to prepare educational sessions for the strategy (team-pair-solo) in practical volleyball lessons for female students and identifying its effect on learning the accuracy of the spiking skill in volleyball. An experimental design with experimental and control groups was employed on a purposive sample of (30) female students who were to constitute (42.254%) from their community represented by the sophomores at the College of Physical Education and Sports Sciences for Girls / University of Baghdad who are in good standing in the morning study for the academic year (2022-2023), whose total number is (71) students. According to the determinants of the experimental design, participants were divided into two equal groups, a

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Publication Date
Sat Sep 16 2023
Journal Name
مجلة الدراسات المستدامة
A Review Article: Use of fertilizers and their gradual release of mineral nutrients as a remedy to this problem have an adverse environmental impact.
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Throughout Agriculture has mostly relied on the use of natural fertilizers throughout human history, which are compounds that increase the nitrogen levels in the soil. Modern agriculture was made possible by the introduction of synthetic fertilizers at the end of the 19th centuryproduction of agriculture. Their application enhanced crop yields and sparked an agricultural revolution unlike anything the world had ever seen.In the near future, synthetic fertilizers are anticipated to continue to have a significant impa ct on human life, both positively and negatively. They are frequently utilized for producing all t ypes of crops and are essential to plant growth. The significance of synthetic fertilizers is their ability to provide the soil w

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Publication Date
Sun Jun 30 2024
Journal Name
Journal Of Current Medical Research And Opinion
Effect of Educational Programs on MothersKnowledge and Childrens Nutritional Status: Narrative Review
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Publication Date
Fri Jul 01 2022
Journal Name
Iop Conference Series: Earth And Environmental Science
Computer Model Application for Sorting and Grading Citrus Aurantium Using Image Processing and Artificial Neural Network
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Abstract<p>This study was conducted in College of Science \ Computer Science Department \ University of Baghdad to compare between automatic sorting and manual sorting, which is more efficient and accurate, as well as the use of artificial intelligence in automated sorting, which included artificial neural network, image processing, study of external characteristics, defects and impurities and physical characteristics; grading and sorting speed, and fruits weigh. the results shown value of impurities and defects. the highest value of the regression is 0.40 and the error-approximation algorithm has recorded the value 06-1 and weight fruits fruit recorded the highest value and was 138.20 g, Gradin</p> ... Show More
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Publication Date
Wed May 10 2017
Journal Name
Australian Journal Of Basic And Applied Sciences
Block-based Image Steganography for Text Hiding Using YUV Color Model and Secret Key Cryptography Methods
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Publication Date
Mon Jul 21 2014
Journal Name
Sensors
Reduction of the Dimensionality of the EEG Channels during Scoliosis Correction Surgeries Using a Wavelet Decomposition Technique
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This paper presents a comparison between the electroencephalogram (EEG) channels during scoliosis correction surgeries. Surgeons use many hand tools and electronic devices that directly affect the EEG channels. These noises do not affect the EEG channels uniformly. This research provides a complete system to find the least affected channel by the noise. The presented system consists of five stages: filtering, wavelet decomposing (Level 4), processing the signal bands using four different criteria (mean, energy, entropy and standard deviation), finding the useful channel according to the criteria’s value and, finally, generating a combinational signal from Channels 1 and 2. Experimentally, two channels of EEG data were recorded fro

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Publication Date
Sun Jan 01 2023
Journal Name
The Egyptian Journal Of Hospital Medicine
The Effect of a Program Using Auxiliary Tools to Improve The Long Passing Skill of Football Juniors
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Publication Date
Mon Sep 30 2024
Journal Name
Modern Sport
The Effect of Skill Exercises According to the Concentration Technique of Lateral Thinking on Motor Accuracy and Learning the Diving Stop Attack for Students in the Epee Weapon
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لمعرفة مدى تأثير تمرينات مهارية وفق تقنية تركيز للتفكير الجاني على الدقة الحركة وتعلم هجمة الإيقاف  بالغطس للطلاب في سلاح الشيش استخدمت الباحثتان المنهج التجريبي على عينة من طلاب المرحلة الثالثة بكلية التربية البدنية وعلوم الرياضة –جامعة ديالى والتي بلغت (30) طالباً موزعين على مجموعتين التجريبية والضابطة وبعد إكمال اجراءات البحث وتطبيق الاختبارات القبلية وتنفيذ التمرينات والاختبار البعدي ومعالجة الب

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Publication Date
Thu Mar 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
(The Segmentation of Industrial Market and its Effect in Targeting Market : An descriptive analytical study for a sample of industrial companies in Iraq)
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 This study deals with segmenting the industrial market as an independent variable and targeting the industrial market as a dependent variable. Since the industrial sector represents one of the most important fundamental pillars to build the economies of countries and their development , the Iraqi industrial sector was chosen as a population for the study . Based on measuring the study variables , identifying them and testing the correlation and effect on each other , the study reached a group of findings:

1- Increasing the level of availability of study variables inside the companies “The study sample”.

2- There is a correlation between the independent v

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