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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 Apr 18 2019
Journal Name
Al-kindy College Medical Journal
Comparative study of anterior knee pain after patelloplasty with and without circumferential denervation in a total knee arthroplasty
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Background: The anterior knee pain is an important chief complaint of the patients with knee osteoarthritis due to patellofemoral pathology. The pain receptors denervation can be achieved by circumferential denervation of the patellar area by a process of electrocautery.

Objectives: The aim of current study is to assess the pain after total knee arthroplasty (TKA) by patelloplastywith and without circumferential denervation via electrocautery at a minimum follow up with 1 year separately for each patient.

Type of the study:Cross- sectional study.

Methods: Thirty five patients,with mean age of about (62.8) years, were enrolled in this pros

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Publication Date
Sun Jan 01 2012
Journal Name
Tikrit Journal For Dental Sciences
Microleakage Evaluation of a Silorane-Based and Methacrylate-Based Packable and Nanofill Posterior Composites (in vitro comparative study)
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This study compared in vitro the microleakage of a new low shrink silorane-based posterior composite (Filtek™ P90) and two methacrylate-based composites: a packable posterior composite (Filtek™ P60) and a nanofill composite (Filtek™ Supreme XT) through dye penetration test. Thirty sound human upper premolars were used in this study. Standardized class V cavities were prepared at the buccal surface of each tooth. The teeth were then divided into three groups of ten teeth each: (Group 1: restored with Filtek™ P90, Group 2: restored with Filtek™ P60, and Group 3: restored with Filtek™ Supreme XT). Each composite system was used according to the manufacturer's instructions with their corresponding adhesive systems. The teeth were th

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Publication Date
Fri Jan 02 2026
Journal Name
Mustansiria Dental Journal
Soft tissue measurements of Iraqi individuals with Cl I and Cl III skeletal pattern: a comparative cephalometric study
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Publication Date
Mon Oct 01 2018
Journal Name
Al–bahith Al–a'alami
Axiology of Electronic programs in updating the methodology of information and communication sciences Tropes 8.4 Case Study
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The study aims to display the scientific benefit offered by modern electronic programs for various scientific research methods, while determining the positive scientific role played by these programs in modernizing the methodologies and logic of scientific thinking, especially with the rapid development of the sciences and their curricula.
These programs link accurately with scientific results. The importance of the study is to provide practical mechanisms to highlight the scientific projection of the electronic programs in various steps of scientific research.
A case study was used for Tropes version 8.4, which analyzes written, audio and visual semantic texts and presents a set of statistical results that facilitate the difficult

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Publication Date
Sat Jun 25 2022
Journal Name
International Journal Of Drug Delivery Technology
Assessment of Serum Levels of the WNT Pathway Antagonist (Dickkopf-1) in a Sample of Type 2 Diabetic Patients with Retinopathy using Two Groups of Antidiabetics
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Objectives: Dickkopf-1 (DKK-1) is WNT/b-catenin pathway antagonist which plays a detrimental role in the development of diabetic retinopathy (DR). This research aimed to assess serum DKK-1 levels in diabetic patients who have and have not developed DR and, compare them with the control subjects finding out whether we can use it as an indicator for DR early diagnosis and to find out which one of the widely used two groups of antidiabetic treatments had the greater effect on this biomarker and hence on the progression of DR. Methods: The study participants were divided into two subgroups: First, 70 patients (36 male, 34 female) with type 2 diabetes mellitus, among them 35 patients diagnosed with DR and 35 with no evidence of DR, and s

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Publication Date
Tue Dec 30 2014
Journal Name
College Of Islamic Sciences
Social solidarity in religions        Three / critical study
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The researcher wanted to make an attempt to identify the foundations of social solidarity, to strengthen the bonds of brotherhood among society, and spread the causes of compassion in the hearts of its members.
       The researcher has taken a short course in the hearts of the beloved to hearts.

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Publication Date
Tue Jan 01 2019
Journal Name
Ieee Access
Implementation of Univariate Paradigm for Streamflow Simulation Using Hybrid Data-Driven Model: Case Study in Tropical Region
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Publication Date
Sun Sep 01 2024
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
The Sensitivity of Immunohistochemical Expression of p53 as an Indicator of the Malignant Potential of Gastric Hyperplastic Polyps: A Retrospective Study
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Background: Hyperplastic polyps account for 30–93% of gastric polyps. Recently, there have been studies about the development of dysplasia in this type of polyp. Every cell in the body contains the p53 gene, which has anti-cancer properties. Objective: The sensitivity of immunohistochemical expression of p53 is evaluated among gastric hyperplastic polyps with and without dysplasia and gastric adenomatous polyps to know its usefulness as a diagnostic marker. Methods: A retrospective cross-sectional study was done on fifty formalin-fixed paraffin-embedded blocks of gastric polyps (44 hyperplastic polyps without dysplasia, 3 hyperplastic polyps with dysplasia, and 3 adenomas). Cases were collected from the archives of the pathology d

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Publication Date
Sat Jun 19 2021
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Serum Chitotriosidase level as a Novel Biomarker for Therapeutic Monitoring of Nephropathic Cystinosis among the Iraqi children
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Background: Cystinosis is a rare autosomal recessive lysosomal storage disease with high morbidity and mortality. It is caused by mutations in the CTNS gene that encodes the cystine transporter, cystinosin, which leads to lysosomal cystine accumulation. It is the major cause of inherited Fanconi syndrome, and should be suspected in young children with failure to thrive and signs of renal proximal tubular damage. The diagnosis can be missed in infants, because not all signs of renal Fanconi syndrome are present during the first months of life. Elevated white blood cell cystine content is the cornerstone of the diagnosis. Since chitotriosidase (CHIT1 or chitinase-1) is mainly produced by activated macrophages both in normal and inflammator

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Publication Date
Sun Sep 01 2019
Journal Name
Baghdad Science Journal
A New Method for the Isolation and Purification of Trigonelline as Hydrochloride from Trigonella foenum-graecum L.
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Separation of Trigonelline, the major alkaloid in fenugreek seeds, is difficult because the extract of these seeds usually contains Trigonelline, choline, mucilage, and steroidal saponins, in addition to some other substances. This study amis to isolate the quaternary ammonium alkaloid (Trigonelline) and choline from fenugreek seeds (Trigonella-foenum graecum L.) which have similar physiochemical properties by modifying of the classical method. Seeds were defatted and then extracted with methanol. The presence of alkaloids was detected by using Mayer's and Dragendorff's reagents. In this work, trigonilline was isolated with traces of choline by subsequent processes of purification using analytical and preparative TLC techniques.

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