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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
Tue Dec 09 2025
Journal Name
Discourse And Interaction
A discursive pragmatic study of emotional blackmail in American movies
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This study examines emotional blackmail from a discursive pragmatic standpoint to gain insights into how this psychologically manipulative phenomenon is revealed in the discourse of some American movies. Five extracts from five American movies are purposely selected and analyzed using an eclectic model based on a discursive pragmatic approach to navigate this unexplored study area. The model incorporates Halliday’s (2014) transitivity system, Martin and White’s (2005) attitude system, Forward and Frazier’s (1997) types and tools of emotional blackmail, and Mayfield’s (2010) informal fallacies. The present study is guided by four research questions that identify the types and tools of emotional blackmail employed in the selec

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Publication Date
Thu Dec 01 2016
Journal Name
Journal Of Cleaner Production
A study of biogas production from date palm fruit wastes
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Publication Date
Mon Feb 11 2019
Journal Name
Journal Of Pharmaceutical Sciences And Research
Design of experiments model for optimization of spectrophotometric determination of phenylephrine hydrochloride in pure and pharmaceutical formulations using p-bromanil
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A simple, fast, inexpensive and sensitive method has been proposed to screen and optimize experimental factors that effecting the determination of phenylephrine hydrochloride (PHE.HCl) in pure and pharmaceutical formulations. The method is based on the development of brown-colored charge transfer (CT) complex with p-Bromanil (p-Br) in an alkaline medium (pH=9) with 1.07 min after heating at 80 °C. ‘Design of Experiments’ (DOE) employing ‘Central Composite Face Centered Design’ (CCF) and ‘Response Surface Methodology’ (RSM) were applied as an improvement to traditional ‘One Variable at Time’ (OVAT) approach to evaluate the effects of variations in selected factors (volume of 5×10-3 M p-Br, heating time, and temperature) on

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Publication Date
Sat Dec 24 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Potential Positive Effects using Coenzyme Q10 Supplement as Adjuvant Therapy to Gabapentin for Managing Diabetic Neuropathy
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The most prevalent chronic complication of diabetes mellitus is diabetic neuropathy. The pathogenesis of diabetic neuropathy is exacerbated by hyperglycemia-induced oxidative stress, which causes nerves to deteriorate in a programmed manner. Many clinical trials depend on supplement in an attempt to improve neuropathy symptoms such as (pain & tingling) and patient quality of life, one of them is Coenzyme Q10 which is reported to have an anti-inflammatory and antioxidant effects, and was totally nontoxic and non-reported side effects. This study aimed to evaluate using a Coenzyme Q10 supplement as an adjuvant therapy to gabapentin to improve the clinical symptoms of diabetic neuropathy in relation to its anti-inflammatory and antioxid

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Publication Date
Fri Feb 06 2026
Journal Name
Journal Of Baghdad College Of Dentistry
The effects of various beverages on the shear bond strength of light-cured orthodontic composite (An in vitro comparative study)
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Background: This study was conducted to assess the effects of various beverages on the shear bond strength of light-cured orthodontic composite used to bond stainless steel orthodontic brackets on human teeth and to determine the site of bonding failure of this material. Materials and Methods: Fifty extracted human premolars were selected and randomly divided into five equal groups each with 10 teeth according to the beverage type (Control, One Tiger, Milk, Green tea and Coffee). After bonding, the teeth were immersed in specific beverages for 5 minutes twice daily with equal intervening intervals then washed and stored in distilled water at 37º C for the reminder of the day. The process was carried out for 30 days. The samples were then

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Publication Date
Thu Sep 18 2025
Journal Name
Sustainable Engineering And Innovation
Using fruit fly and dragonfly optimization algorithms to estimate the Fama-MacBeth model
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This research proposes the application of the dragonfly and fruit fly algorithms to enhance estimates generated by the Fama-MacBeth model and compares their performance in this context for the first time. To specifically improve the dragonfly algorithm's effectiveness, three parameter tuning approaches are investigated: manual parameter tuning (MPT), adaptive tuning by methodology (ATY), and a novel technique called adaptive tuning by performance (APT). Additionally, the study evaluates the estimation performance using kernel weighted regression (KWR) and explores how the dragonfly and fruit fly algorithms can be employed to enhance KWR. All methods are tested using data from the Iraq Stock Exchange, based on the Fama-French three-f

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Publication Date
Sun Feb 05 2017
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
STUDY THE OPTIMUM CONDITIONS FOR THE REMOVAL OF HEAVY METAL ELEMENTS FROM AQUEOUS SOLUTIONS USING CONTAMINATED BACTERIA Bacillus subtilis LOCALLY ISOLATED: STUDY THE OPTIMUM CONDITIONS FOR THE REMOVAL OF HEAVY METAL ELEMENTS FROM AQUEOUS SOLUTIONS USING CONTAMINATED BACTERIA Bacillus subtilis LOCALLY ISOLATED
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We studied the effect of certain environmental conditions for removing heavy metal elements from contaminated aqueous solutions (Cd, Cu, Pb, Fe, Zn, Ni, Cr) using the bacterium Bacillus subtilis to appoint the optimal conditions for removal ,The best optimum temperature range for two isolate was 30-35○C while the hydrogen number for the maximum mineral removal range was 6-7. The best primary mineral removal was 100 mg/L, while the maximum removal for all minerals was obtained after 6 hrs of Cu element time and the maximum removal efficiency was obtained after 24 hrs of Cu element. The results have proved that the best aeration for maximum removal was obtained at rotation speed of 150 rpm/minute. Inoculums of 5ml/100ml which contained 1

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Publication Date
Wed Aug 07 2019
Journal Name
Iraqi National Journal Of Nursing Specialties
Quality of Life for Adult Clients with Hypermobility Syndrome Attending Private Clinics in Baghdad City: A Cross-Sectional Study
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Objective)s): To evaluate the quality of life for adult clients with hypermobility syndrome at private clinics in Baghdad City. Methodology: A cross-sectional study used a purposive ‘’non-probability’’ sample of (75) adult clients with Hypermobility Syndrome (HMS) male and female who age (25-64) years. The data were collected through the utilization of standard developed questionnaire of the world health organization (WHO). Data collected by interview with each client who is involved in the study. Each interview takes approximately (20) minutes. Results: The study revealed that there is an effect of hypermobility syndrome on the quality of life, which recorded fair level in general. The study also reported that there is an effect

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Publication Date
Fri Feb 06 2026
Journal Name
Al–bahith Al–a'alami
Petra University’s Students’ Uses For SMS Messages and its Verifications (A Field Study on Students of Petra University’s Colleges)
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This study aims at identifying the extent of SMS usage and understanding the role it plays in satisfying users' needs and motivations. In order to achieve this aim, an analytical descriptive method was adopted by conducting a field survey among students at Petra University.

The study resulted in many conclusions, the most important of which is that using SMS meets the students' cognitive, social and communicational needs and desires, the highest being communicating with friends at 75%, followed by exchanging songs and videos at 52%, as well as exchanging photos at 45%. In regards to their motivation for using text messaging, forgetting daily problems scored highest at 81.4% and spending free time followed at 77.4%. This proves th

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Publication Date
Tue Mar 30 2021
Journal Name
Baghdad Science Journal
Diversity Assessment by Molecular Barcoding and Seed Morphology in Ricinus communis L.: Molecular diversity of Ricinus seeds
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Fourteen morphologically varied Ricinus communis L. seeds were collected from different localities in Egypt, El-Sudan and Saudi Arabia. Seed morphology and ITS barcoding analysis were performed to assess their diversity and phylogenetic relationship. Sequence’s alignment of nrITS region from different accessions display high levels of genetic similarities. Cluster analysis could not group different accessions according to their geographical distribution. Nevertheless, the genetic barcodes are interestingly matched with the morphological features of the Ricinus seeds. In conclusion, seed morphology proved to be a valuable tool in evaluating biodiversity and phylogenetic relationship in plant species with different loca

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