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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
Fri Jan 05 2018
Journal Name
Asian Quarterly: An International Journal Of Contemporary Issue
Refugees and the Challenges for Language Education (LE): A Theoretical Study
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DBN Rashid, Asian Quarterly: An International Journal of Contemporary Issue, 2018

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Publication Date
Mon Jan 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
‘There is no place like home’: A Comparative Study of the Meaning of Home in The Wonderful Wizard of Oz and Peter and Wendy
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The Wonderful Wizard of Oz and Peter and Wendy present universal ideas that exist in all times, despite being written in the beginning of the 20th century. Among the most significant ones is the concept of “home”. The article discusses the essentiality of the idea of “home” where the identity of an individual shapes, and where one’s spiritual, psychological, and physical being develop. It also studies the attitudes of each protagonist towards the concept of ‘home’ based on their understanding of it and according to their gender differences. The characters in both stories tread on the path of perplexity between leaving their homes and returning to them. Peter’s world is the world of imagination while Doro

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Publication Date
Wed Dec 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Comparative Evaluation of the Effect of Different Universal Adhesives and Bonding Techniques on the Marginal Gap of Class I Composite Restoration (A SEM Study)
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Background: With the increase in composite material use in posterior teeth, the concerns about the polymerization shrinkage has increased with the concerns about the formation of marginal gaps in the oral cavity environment. New generation of adhesives called universal adhesive have been introduced to the market in order to reduce the technique sensitive bonding procedures to give the advantage of using the bonding system in any etching protocol without compromising the bonding strength. The aim of the study was to study marginal adaptation of two universal adhesives (Single bondâ„¢ Universal and Prime and Bond elect) using 3 etching techniques under thermal cycling aging. Materials and Methods: Forty-eight sound maxillary first premola

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Publication Date
Thu May 25 2023
Journal Name
Results In Chemistry
Synthesis and characterization of (E)-4-(((4-(5-mercapto-1, 3, 4-oxadiazol-2-yl) phenyl) amino) methyl)-2-methoxyphenol as a novel corrosion inhibitor for mild-steel in acidic medium
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Metal corrosion is a destructive process for many industrial operations, including oil well acidizing and acid pickling. Therefore, numerous efforts made by many researchers to control the steel corrosion. In the present work, A (E)-4-(((4-(5-mercapto-1,3,4-oxadiazol-2-yl) phenyl) amino) methyl)-2-methoxyphenol (MOPM) has been synthesized and characterized as a new corrosion inhibitor for mild steel in 0.1 M hydrochloric acid. FTIR and 1 HNMR were used in the diagnosis of MOPM, while electrochemical polarization technique was employed to test the performance of inhibitor at various temperatures and inhibitor concentrations. Electrochemical studies showed that MOPM acts as a mixed-type inhibitor with a maximum inhibition efficiency of

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Publication Date
Sun Jan 01 2023
Journal Name
Results In Chemistry
Synthesis and characterization of (E)-4-(((4-(5-mercapto-1, 3, 4-oxadiazol-2-yl) phenyl) amino) methyl)-2-methoxyphenol as a novel corrosion inhibitor for mild-steel in acidic medium
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Publication Date
Mon Jul 10 2023
Journal Name
Journal Of Engineering
Rhythm As Creative System In Houses Architecture Comparative Application Study Between Heritage And Contemporary Houses
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Rhythm is considered one of the creative concepts in the recent architectural thought; it has emerged clearly as a mean of creating the highest levels of creativity in architecture, especially in contemporary architectural movements. The importance of rhythm has  emerged, especially, when the architecture , its beginnings concentrated on the principle of the links with poetic structures. Many architectural studies deal with concept of rhythm in architecture with different ways various according to the trend of each study, this show the importance of studying the concept of rhythm in the architectural field in general. This study try to focus on the utilization of rhythm as creative system in architecture of heritage and contemporary

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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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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
Mon Dec 25 2017
Journal Name
Al-khwarizmi Engineering Journal
A new Cumulative Damage Model for Fatigue Life Prediction under Shot Peening Treatment
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 Abstract

In this paper, fatigue damage accumulation were studied using many methods i.e.Corton-Dalon (CD),Corton-Dalon-Marsh(CDM), new non-linear model and experimental method. The prediction of fatigue lifetimes based on the two classical methods, Corton-Dalon (CD)andCorton-Dalon-Marsh (CDM), are uneconomic and non-conservative respectively. However satisfactory predictions were obtained by applying the proposed non-linear model (present model) for medium carbon steel compared with experimental work. Many shortcomings of the two classical methods are related to their inability to take into account the surface treatment effect as shot peening. It is clear that the new model shows that a much better and cons

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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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