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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
Sat Jun 06 2020
Journal Name
Journal Of The College Of Education For Women
A Critical Pragmatic Study of Racism as Conceptualized in the Glorious Quran
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Racism changes its meaning, shape, purpose or function according to various factors such as time, place, motives, and backgrounds; among others. It seems, however, to have deep roots back in the history of mankind. Such a concept stems from a perceived difference with the other. It is fed by the feeling of being hierarchically superior in opposition to another party that is depicted as inferior. Since ancient times, racism is disguised in different forms and manifests itself on various levels. It is a truism that this ideology can be best presented via language.

Due to its negative implication, racism lends itself to a critical kind of research.  As such, this paper is a critical pragmatic investigation for this phenomenon a

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Publication Date
Thu Feb 19 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Accuracy of spiral computed tomography in evaluation of maxillary sinus septa among dentate and edentulous Iraqi subjects (Comparative study)
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Background: Presence of maxillary sinus septa has been known to be a complicating factor for sinus elevation procedure and implant placement in posterior maxilla. The maxillary sinuses septa are thin walls of cortical bone inside the sinus. They vary in number, location, and height. This study aimed to discover the accuracy of Spiral Computed Tomographic Scan in evaluation the maxillary sinus septa (prevalence, location, height) in subjects with dentate, partially edentulous and completely edentulous maxilla. Material and method: This study included (267) subjects ranged from (20-70 years), (132) male and (135) female divided into three groups, (97) fully dentate group, (102) partially edentulous group and (68) completely edentulous group w

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Publication Date
Thu Feb 19 2026
Journal Name
Journal Of Baghdad College Of Dentistry
The effect of curvature angle and rotational speed on the cyclic fatigue of three types of rotary instrument (In vitro): comparative study
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Background: The fracture of instruments within root canal during endodontic treatment is a common incidence, fracture because of fatigue through flexure occurs due to metal fatigue, this study aimed to assess the effect of curvature angle and rotational speed on the cyclic fatigue of different type of Endodontic NiTi Rotary Instruments and compare among them. Materials and method: Three types of rotary instruments with tip size 0.25: ProTaPer F2 (Densply, Malifier) Revo-S SU( 0.06 taper, MicroMega) and RaCe system (0.06 taper, FKG, Dentaire), Forty file of each instrument were used within two canals with angle of curvature (40 &60 )at two speed (250&400)RPM, twelve group were formed for all instruments(total number=120),ten file fo

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Publication Date
Wed Aug 27 2025
Journal Name
Al-salam Journal For Medical Science
Nanotechnology in Molecular Genetics: A literature review
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Nanotechnology extends the limits of molecular diagnostics to the nanoscale. This study describes some of the details of how the body interacts with nanoparticles. Biological tests measuring the presence or activity of selected substances become quicker, more sensitive, and more flexible when certain nanoscale particles are put to work as tags. Particular emphasis is placed on the effects of surface changes on body-borne particles, their transport within the body, and the dose-response effect. Other considerations include the definition of "persistent" in the context of therapy, FDA scientific committees, and the need for nanoparticle tracking. In short, there have been dramatic changes in molecular and genetic research findings, as well as

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Publication Date
Sat Jan 01 2022
Journal Name
Acta Facultatis Medicae Naissensis
Asthma as a risk factor for The progression of COVID-19
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Background: Asthma is one of the most common chronic respiratory diseases in the world, standing for the most frequent cause for hospitalization and emergency cases. Respiratory viruses are the most triggering cause. Aim: To assess the role of viral infections, especially COVID-19, in the pathogenesis of asthma initiation and exacerbations. Method: Electronic search was done for the manuscripts focusing on asthma as a risk factor for complications after COVID-19 infection. The outcomes were titles, materials, methods and classified studies related or not related to the review study. Three hundred publications were identified and only ten studies were selected for analysis. Seven studies were review, one retrospective, one longitudin

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Publication Date
Sun Jun 30 2019
Journal Name
Journal Of The College Of Education For Women
Physical Identity in the Marshes Chabaish District as a Case Study
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The marshes form large areas in southern Iraq, which are large water bodies, covered by reeds and papyrus plants. The marshes are characterized by distinctive physical elements, which have given them a unique and unique identity that can be clearly distinguished by the physical pattern. The physical environment derives its identity through a group Of inputs that interact with each other and represent both cultural and social inputs of the most important inputs that affect the formation of identity, and in the physical environment of the Marshlands many of the symbols that are associated with the collective memory of individuals, these symbols have value in the community Thus, the preservation of these symbols and inherited from one gener

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Publication Date
Sun Mar 08 2020
Journal Name
Biochem. Cell. Arch
SYNTHESIS AND SPECTROSCOPIC CHARACTERIZATION OF NEW HETEROCYCLIC COMPOUNDS DERIVATIED FROM 1-(4-AMINOPHENYL) ETHAN-1-ONEOXIME AS A STARTING MATERIAL WITH EVALUATE THEIR BIOLOGICAL ACTIVITY
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ABSTRACT : This research involves the synthesis of five to seven heterocyclic compounds starting with Schiff’s bases which derived from oxime as a starting material. 1.3-oxazepine derivatives were prepared from adding different anhydrides to the Schiff bases, tetrazole and thiazolidinone derivatives synthesized from add sodium azide and thioglycolic acid to the same Schiff’s bases as a five members ring. Pyrimidine derivatives were prepared after the reaction of the azomethine group with acetyl chloride and then urea and thiourea to synthesis on derivatives contain the six members ring. Another step included identified and confirmed these compounds by FT- IR, 1HNMR, TLC and 13CNMR finally, step included the assay of biological activity

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Publication Date
Sun Jun 23 2019
Journal Name
American Rock Mechanics Association
Using an Analytical Model to Predict Collapse Volume During Drilling: A Case Study from Southern Iraq
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Zubair Formation is one of the richest petroleum systems in Southern Iraq. This formation is composed mainly of sandstones interbedded with shale sequences, with minor streaks of limestone and siltstone. Borehole collapse is one of the most critical challenges that continuously appear in drilling and production operations. Problems associated with borehole collapse, such as tight hole while tripping, stuck pipe and logging tools, hole enlargement, poor log quality, and poor primary cement jobs, are the cause of the majority of the nonproductive time (NPT) in the Zubair reservoir developments. Several studies released models predicting the onset of borehole collapse and the amount of enlargement of the wellbore cross-section. However, assump

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Publication Date
Tue Jan 01 2019
Journal Name
The 53rd U.s. Rock Mechanics/geomechanics Symposium
Using an analytical model to predict collapse volume during drilling: A case study from southern Iraq
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Publication Date
Sun Jun 05 2011
Journal Name
Baghdad Science Journal
A Study of Some Physical Properties for Binary System of Cyclohexane with n-decane and 1-pentanol at Different Temperatures
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mixtures of cyclohexane + n-decane and cyclohexane + 1-pentanol have been measured at 298.15, 308.15, 318.15, and 328.15 K over the whole mole fraction range. From these results, excess molar volumes, VE , have been calculated and fitted to the Flory equations. The VE values are negative and positive over the whole mole fraction range and at all temperatures. The excess refractive indices nE and excess viscosities ?E have been calculated from experimental refractive indices and viscosity measurements at different temperature and fitted to the mixing rules equations and Heric – Coursey equation respectively to predict theoretical refractive indices, we found good agreement between them for binary mixtures in this study. The variation of th

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