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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 Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
An Evaluative study for the Arabic language course program: An Evaluative study for the Arabic language course program
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Abstract
Language is one of God’s blessings to human beings through which he
distingushed them from other creatures, then how if this language was arabic.
God honored this language and in which he descended his Gracious Boole
that gave it glory and magnificance, and made it an immortal revelation to the
arab nation in their poetry, oration, history and human tendency to the life of
knowledge, mind leadershipe, innovation and progress.
This study aimed at evaluating the arabic language come program for
the new teachers. The sample was of (25) participants who were shown a
questionaire consisting of (60) items distributed on (9) fields. Then, the data
was processed statisically by using preauency rate, Kai s

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Publication Date
Mon Nov 24 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Validity of computed tomographic in assessment of genial tubercle and anterior mandible as a reference guide to locate osteotomy in genioglossus advancement
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Background: Genioglossus advancement is a surgical procedure to advance the tongue in some patients with obstructive sleep apnea syndrome.The important step in this procedure is that of accurately capturing the bone segment attached to the genioglossus muscle to avoid complications such as mandibular fracture, devitalization of the inferior incisor roots, and incomplete incorporation of the genioglossus Materials and Method: Computed tomography scans were taken for 53 Iraqi adult patients (28 male and 25 female) range from (18-35) years with skeletal class I classification and intact anterior mandible dentition included in this study using sagittal and axial sections. The measurements were done for genial tubercle and anterior mandibular re

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Publication Date
Sat Sep 28 2024
Journal Name
Journal Of The Pakistan Medical Association
Pulse transmission time and amplitude of digital pulse wave determined by fingertip plethysmography as a surrogate marker of brachial artery flowmediated dilatation
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Objectives: To assess the changes in blood vessel stiffness and digital pulse wave amplitude because of flowmediateddilatation, and to explore how these two variables change when endothelial dysfunction isexperimentally induced.Method: The experimental study was conducted at the departments of physiology at the College of Medicine,Mustansiriyah University, and the College of Medicine, Al-Iraqia University, Baghdad, Iraq, from October 14, 2021, toMay 31, 2022, and comprised healthy young males who were subjected to the flow-mediated dilatation techniqueon the left brachial artery. Pulse transit time and the amplitude of the digital pulse wave were measured duringreactive hyperaemia for 2.5 minutes from the left middle finger using a

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Publication Date
Mon Nov 24 2025
Journal Name
Journal Of Baghdad College Of Dentistry
The effect of orthodontic relapse on the proliferation of fibroblast and epithelial rests of Malassez in periodontal ligament of rat molars (A histopathological study)
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Background: Relapse of previously moved teeth, is major clinical problem in orthodontics with respect to the goals of successful treatment. This study investigated the effect of orthodontic relapse on the proliferation of fibroblast and epithelial rests of Malassez cells in periodontal ligament of rat molars. Materials and Methods: Sixteen ten-week- old male Wister rats were randomly divided into four groups composed of four animals each: Group I received no orthodontic force (control). In both Group II and Group III, uniform standardized expansive springs were used for moving the maxillary first molars buccally for periods of one and three weeks respectively. The spring initially generated an average expansive force of 20 g on each side.

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Publication Date
Wed Apr 01 2020
Journal Name
International Journal Of Pharmaceutical Research
Molecular Interaction in Aqueous Solution of Butanol Isomers at 298.15 K
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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Morphological, Molecular and Pollen Grain Investigations of Salix Species in Egypt
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Genus Salix is among family Salicaceae, distributing in the northern hemisphere. It is represented in Egypt by two species (Salix mucronata and Salix tetrasperma). The classification of Salix at the generic and infra-generic levels is still outstanding. We have agreed to list the Egyptian species of this genus. We collected them during field trips to most Egyptian habitats; fresh and herbarium specimens were subjected to taxonomic revision based on morphological characters; scanning electron microscope (SEM) for pollen grains; isozyme analysis using esterase and peroxidase enzymes and genetic diversity using random amplified polymorphic DNA (RAPD). We recorded that both sexes of S.

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Publication Date
Fri Jan 10 2020
Journal Name
International Journal Of Pharmaceutical Research
Molecular Interaction in Aqueous Solution of Butanol Isomers at 298.15 K
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Viscosity (η) of solutions of 1-butanol, sec-butanol, isobutanol and tert-butanol were investigated in aqueous solution structures of ranged composition from 0.55 to 1 mol.dm-3 at 298.15 K. The data of (η/η˳) were evaluated based on reduced Jone - Dole equation; η/η˳ =BC+1. In the term of B value, the consequences based on solute-solvent interaction in aqueous solutions of alcohols were deliberated. The outcomes of this paper discloses that alcohols act as structure producers in the water. Additionally, it has shown that solute-solvent with interacting activity of identical magnitude is in water-alcohol system

Publication Date
Wed Apr 01 2020
Journal Name
International Journal Of Pharmaceutical Research
Molecular Interaction in Aqueous Solution of Butanol Isomers at 298.15 K
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Publication Date
Sat Jan 21 2023
Journal Name
Eastern Journal Of Agricultural And Biological Sciences
Isolation and molecular identification of Pathogenic cryptococcus gattii from natural habitat
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This study is designed to isolate and molecular identification of C. gattii, C. gattii is pathogenic yeast and effect immunocomposed and immunocompetent, Methods: collect 50 samples from eucalyptus leaves. The collection time was extended from November 2021 to February 2022 and then culture at SDA, Cryptococcus Differential Agar esculin agar and Eucalyptus leaves agar, Brain heart infusion agar with methyldopa and Brain heart infusion agar with methyldopa media, biochemical test including urease test, and then confirm identification by molecular identification by PCR technique sequencing and genetic analysis. The results showed that 4 swaps taken from eucalyptus leaves included cryptococcus neoformans. This study indicated that the virulenc

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Publication Date
Tue May 11 2021
Journal Name
Egyptian Journal Of Medical Human Genetics
Molecular analysis of CFTR gene mutations among Iraqi cystic fibrosis patients
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Abstract<sec> <title>Background

Cystic fibrosis (CF) is an autosomal recessive multisystem disease that results from mutation(s) of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. More than 2100 mutations and polymorphisms have been reported in this gene so far. Incidence and genotyping of CF are under-identified in Iraq. This study aims to determine the types and frequencies of certain CFTR mutations among a sample of Iraqi CF patients. Two groups of patients were included: 31 clinically confirmed CF patients in addition to 47 clinically suspected patients of CF. All confirmed pa

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