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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 Mar 21 2024
Journal Name
International Development Planning Review
THE EFFECT OF USING A DISABLING FORCE TRAINING TOOL ON WALKING PERFORMANCE: AN ANALYTICAL STUDY OF TIME AND STEP LENGTH IN THE 20 KM WALKING RACE EVENT FOR APPLICANTS
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Publication Date
Wed Mar 18 2020
Journal Name
Baghdad Science Journal
Spectrophotometric and Reverse Flow Injection Method Determination of Nitrazepam in Pharmaceuticals Using O-Coumaric Acid as a New Chromogenic Reagent
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            A spectrophotometric- reverse flow injection analysis (rFIA) method has been proposed for the   determination of Nitrazepam (NIT) in pure and pharmaceutical preparations. The method is based upon the coupling reaction of NIT with a new reagent O-Coumaric acid (OCA) in the presence of sodium periodate in an aqueous solution. The blue color product was measured at 632 nm. The variation (chemical and physical parameters) related with reverse flow system were estimated. The linearity was over the range 15 - 450 µg/mL of NIT with detection limits and limit of quantification of 3.425 and 11.417 µg mL-1 NIT,respectively. The sample throughput of 28 samples

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Publication Date
Mon Nov 21 2022
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn: 2789-3219 )
Nanotechnology at the Molecular Level
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Materials with external dimensions of one or more nanometers are referred to as nanomaterials. These structures result from a number of manufacturing processes. They are used in many industries, including pharmaceuticals, which is the most significant one. Numerous variables, including size, shape, surface morphology, crystallinity, solubility, etc., affect physical properties. While new physical and chemical processes are being created constantly, the biological method is the ideal strategy for synthesizing nanoparticles since it is straightforward, safe, and economical. Different kinds of nanoparticles can be metabolically synthesized by a wide variety of biological sources, including plants, bacteria, fungi, and yeast. There are

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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Molecular study of the relationship of gene expression of some genes with the temperature variation of bacterial growth
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Pseudomonas aeruginosa is an opportunistic pathogen responsible for serious infections. At least three different exopolysaccharides, alginate, polysaccharide synthesis locus (Psl), and pellicle exopolysaccharide (Pel) make up the biofilm matrix in P. aeruginosa . The effect of temperature on the biofilm formation and gene expression was examined by microtiter plate and real-time quantitative polymerase chain reaction (qRT-PCR). To be able to determine the effect of temperature on biofilm formation and gene expression of P. aeruginosa, 303 clinical and environmental samples were collected. Pseudomonas aeruginosa was isolated from 61 (20.1%) and 48 (15.8%) of the clinical and e

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Publication Date
Mon Apr 01 2024
Journal Name
Iraqi Journal Of Oil And Gas Research (ijogr)
Comparative study of electrochemical oxidation system hybrid with photocatalytic system for the treatment of Al-Najaf petroleum refinery wastewater
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Publication Date
Thu Apr 03 2025
Journal Name
Isa Transactions
Optimal hybrid type-3 fuzzy controller for horizontal axis wind turbines: Comparative study
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The blade pitch angle (BPA) controller is key factor to improve the power generation of wind turbine (WT). Due to the aerodynamic structural behavior of the rotor blades, wind turbine system performance is influenced by pitch angle and environmental conditions such as wind speed, which fluctuate throughout the day. Therefore, to overcome the pitch angle control (PAC) problem, high wind speed conditions, and due to type-1 and type-2 fuzzy logic limitations for handling high levels of uncertainty, the newly proposed optimal hybrid type-3 fuzzy logic controller has been applied and compared since type-3 fuzzy controllers utilize three-dimensional membership functions, unlike type-2 and type-1 fuzzy logic controllers. In this paper six differen

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Publication Date
Mon Jan 01 2024
Journal Name
Baghdad Science Journal
Classification of Arabic Alphabets Using a Combination of a Convolutional Neural Network and the Morphological Gradient Method
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The field of Optical Character Recognition (OCR) is the process of converting an image of text into a machine-readable text format. The classification of Arabic manuscripts in general is part of this field. In recent years, the processing of Arabian image databases by deep learning architectures has experienced a remarkable development. However, this remains insufficient to satisfy the enormous wealth of Arabic manuscripts. In this research, a deep learning architecture is used to address the issue of classifying Arabic letters written by hand. The method based on a convolutional neural network (CNN) architecture as a self-extractor and classifier. Considering the nature of the dataset images (binary images), the contours of the alphabet

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Publication Date
Fri Jun 01 2018
Journal Name
Iraqi Journal Of Science
Cleavage of mucin and salivary agglutinin by partiallypurified protease from native strain of Streptococcus mutansan67
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Publication Date
Tue Mar 26 2024
Journal Name
Scientific Reports
An in vitro assessment of the residual dentin after using three minimally invasive caries removal techniques
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Abstract<p>To evaluate the efficiency and effectiveness of three minimally invasive (MI) techniques in removing deep dentin carious lesions. Forty extracted carious molars were treated by conventional rotary excavation (control), chemomechanical caries removal agent (Brix 3000), ultrasonic abrasion (WOODPECKER, GUILIN, China); and Er, Cr: YSGG laser ablation (BIOLASE San Clemente, CA, USA). The assessments include; the excavation time, DIAGNOdent pen, Raman spectroscopy, Vickers microhardness, and scanning electron microscope combined with energy dispersive X-ray spectroscopy (SEM–EDX). The rotary method recorded the shortest excavation time (p < 0.001), Brix 3000 gel was the slowest. DIAGNOdent pen va</p> ... Show More
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Publication Date
Fri Jul 01 2016
Journal Name
Journal Of Engineering
Determination of Mono-crystalline Silicon Photovoltaic Module Parameters Using Three Different Methods
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For modeling a photovoltaic module, it is necessary to calculate the basic parameters which control the current-voltage characteristic curves, that is not provided by the manufacturer. Generally, for mono crystalline silicon module, the shunt resistance is generally high, and it is neglected in this model. In this study, three methods are presented for four parameters model. Explicit simplified method based on an analytical solution, slope method based on manufacturer data, and iterative method based on a numerical resolution. The results obtained for these methods were compared with experimental measured data. The iterative method was more accurate than the other two methods but more complexity. The average deviation of

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