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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
Sun Aug 28 2022
Journal Name
Geodesy And Cartography
OBJECT-BASED APPROACHES FOR LAND USE-LAND COVER CLASSIFICATION USING HIGH RESOLUTION QUICK BIRD SATELLITE IMAGERY (A CASE STUDY: KERBELA, IRAQ)
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Land Use / Land Cover (LULC) classification is considered one of the basic tasks that decision makers and map makers rely on to evaluate the infrastructure, using different types of satellite data, despite the large spectral difference or overlap in the spectra in the same land cover in addition to the problem of aberration and the degree of inclination of the images that may be negatively affect rating performance. The main objective of this study is to develop a working method for classifying the land cover using high-resolution satellite images using object based method. Maximum likelihood pixel based supervised as well as object approaches were examined on QuickBird satellite image in Karbala, Iraq. This study illustrated that

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Publication Date
Sat Jan 24 2026
Journal Name
Misan Journal For Physical Education Sciences
The impact of three models of training load on the development of the maximum strength for elite boxers
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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
Mon Dec 22 2025
Journal Name
Wasit Journal For Pure Science
Synthesis, Characterization and Study of Liquid Crystal Behavior of Linear-Shaped Mesogens Containing Cyano and Alkyl as a Terminal Groups
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A novel series of liquid crystalline compounds containing 2,4-thiazolidinedione units with varying terminal alkyl chain lengths was successfully synthesized and characterized. The chemical structures of the synthesized compounds were confirmed by FT-IR, ¹H-NMR, and mass spectrometry. The mesomorphic behavior was investigated using polarized optical microscopy (POM) and differential scanning calorimetry (DSC). Compounds [V]₄, [V]₅, and [V]₆ exhibited enantiotropic nematic phases, while compound [V]₈ displayed a smectic A (SmA) phase. No liquid crystalline behavior was observed for compound [V]₃. The liquid crystalline properties were found to depend on the terminal-to-lateral chain length ratio, molecular geometry, and the nature

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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 Jan 01 2021
Journal Name
Research Journal Of Pharmacy And Technology
Bacteriological and molecular study on S. Aureus bacteria Atala, M.L.
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Publication Date
Tue Oct 01 2019
Journal Name
Environmental Earth Sciences
Urban geochemistry assessment using pollution indices: a case study of urban soil in Kirkuk, Iraq
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Publication Date
Fri Aug 02 2019
Journal Name
The Fifth Conference On Smart Monitoring, Assessment And Rehabilitation Of Civil Structures Smar 2019
Rehabilitation of Mohammed Al-Qassim Bridge after Fire Attack Using CFRP Sheets: A Case Study
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Publication Date
Wed May 17 2023
Journal Name
College Of Islamic Sciences
The origins of the structure of nominative pronouns, a linguistic study
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The Arabic pronouns received a lot of attention from the ancient Arab grammarians, so they explained their origins, the different forms of their structure, and the aspects of the Arabs’ use of them, and explained the aspects and reasons for these uses, with what they had of linguistic insight, which guided them to clarify the truth of these pronouns.
And recently, this research seeks new knowledge of the development of the structure of the nominative pronouns (he), (she), (them), (taa), and (waw) between dialects and towards classical Arabic, by analyzing the structure of these pronouns into their components. Its linguistic formulas are traced from the ancient Arabic texts, and by ancient I mean the texts of the era of linguistic ci

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Publication Date
Tue Dec 31 2019
Journal Name
Biochemical & Cellular Archives
8-HYDROXY-2-DEOXY GUANOSINE IS A NOVEL NEW BIOCHEMICAL MARKER FOR PATIENTS WITH MULTIPLE SCLEROSIS AND CORRELATION WITH PARAOXANASE-1 AND MDA
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Multiple sclerosis (MS) is a chronic, inflammatory demyelinating disease of central nervous system with complex etiopathogenesis that impacts young adults (Lee et al., 2015), and MS impacts younger and middle aged character and leads to a range of disabilities that can alter their daily routines (Yara et al, 2010). Although, the exact cause of MS is still undetermined, the disease is mediated by adaptive immunity through the infiltration of T cells into the central nervous system (Bjelobaba et al, 2017). MS causes the Focal neurological symptomsand biochemical changes in the molecular level and the variation of neural cells such as loss or alteration of sensation, motor function, visible signs such as blurred vision or transient blindness,

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