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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
Sun Oct 07 2018
Journal Name
Al-kindy College Medical Journal
Risedronate as a therapeutic trial post-hysterectomy in premenopausal women to prevent osteoporosis
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Background: Osteoporosis is a skeletal defect manifested by a reduction of bone strength as a result of reduced bone mass to the extent that there is a higher risk of fracture even on minor trauma. Hysterectomy in a premenopausal woman is a well known cause of ovarian failure resulting in an increased risk of osteoporosis.

Objective : To clarify bisphosphonate's preventive effect on osteopenia and osteoporosis in premenopausal women after hysterectomy.

Type of the study: Cross –sectional study.

Method:  84 premenopausal females post hysterectomy aged between 40 – 50 years, were enrolled in this randomized controlled double blinded trail a

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Publication Date
Mon Jun 26 2023
Journal Name
Journal Of Contemporary Medical Sciences
Glyceryl Trinitrate, a Vasodilating Drug Acts as an Antibiofilm Agent in Serratia marcescens
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Objectives: Serratia marcescens is a gram-negative pathogen of many species. The ability of S. marcescens to form biofilms and its potent innate resistance to antimicrobials and cleaning solutions are both essential for its pathogenicity and survival. The present study was conducted to investigate the effect of glyceryl trinitrate (GTN) on the biofilm of S. marcescens, as an alternative for antibiotic therapy. Methods: Different specimens, including ear swabs, burns, mid-stream urine, wound swabs, and sputum, were collected from patients who were brought to Al-Ramadi Hospital, Iraq. All samples were cultured, and the colonies that were obtained were detected using the VITEK® 2 compact. The ability of biofilms to develop was e

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Publication Date
Sat Jan 01 2022
Journal Name
3rd International Scientific Conference Of Alkafeel University (iscku 2021)
Investigations for the critical vehicle velocities on a curved path
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􀀨􀀅􀀆􀀔􀀜􀀄􀀂􀀆􀀈􀀓􀀌􀀩􀀏􀀆􀀉􀀅􀀆􀀉􀀅􀀉􀀚􀀝􀀔􀀄􀀗􀀉􀀚􀀆􀀂􀀓􀀚􀀁􀀔􀀄􀀓􀀅􀀆􀀄􀀂􀀆􀀔􀀓􀀆􀀃􀀂􀀔􀀄􀀟􀀉􀀔􀀃􀀆􀀔􀀜􀀃􀀆􀀛􀀃􀀜􀀄􀀗􀀚􀀃􀀆􀀗􀀌􀀄􀀔􀀄􀀗􀀉􀀚􀀆􀀂􀀘􀀃􀀃􀀊􀀂􀀆􀀓􀀖􀀆􀀓􀀛􀀃􀀌􀀔􀀁􀀌􀀅􀀄􀀅􀀕􀀢􀀆􀀪􀀜􀀃􀀆􀀄􀀅􀀛􀀃􀀂􀀔􀀄􀀕􀀉􀀔􀀄􀀓􀀅􀀂􀀆 􀀉􀀌􀀃􀀆􀀙􀀉􀀂􀀃􀀊􀀆􀀓􀀅􀀆􀀉􀀁􀀔􀀓􀀟􀀓􀀙􀀄􀀚􀀃􀀆􀀚􀀉􀀔􀀃􀀌􀀉􀀚􀀆􀀂􀀘􀀉􀀗􀀃􀀆􀀟􀀄􀀊􀀂􀀔􀀆􀀔􀀜􀀃􀀆􀀗􀀃􀀅􀀔􀀃􀀌􀀚􀀄􀀅􀀃􀀂􀀆􀀓􀀖􀀆􀀔􀀜􀀃􀀆􀀙􀀉􀀂􀀃􀀆

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Publication Date
Fri Mar 01 2019
Journal Name
Al-khwarizmi Engineering Journal
A Finite Element Analysis for the Damaged Rotating Composite Blade
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In this paper, the finite element method is used to study the dynamic behavior of the damaged rotating composite blade. Three dimensional, finite element programs were developed using a nine node laminated shell as a discretization element for the blade structure (the same element type is used for damaged and non-damaged structure). In this analysis the initial stress effect (geometric stiffness) and other rotational effects except the carioles acceleration effect are included.  The investigation covers the effect speed of rotation, aspect ratio, skew angle, pre-twist angle, radius to length, layer lamination and fiber orientation of composite blade. After modeling a non-damaged rotating composite blade, the work procedure was to ap

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Publication Date
Mon Sep 03 2018
Journal Name
Al-academy
A new vision for the classic in contemporary fashion designResearch
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        fashion designers who have benefited greatly from the mobilization of ancient aesthetic ideas in the heritage of the people and guaranteed in their productions so that there is no change In the aesthetic value created by the designers of the research in the ancient heritage to find new signs that reflect the connection of man to the present as the aesthetic value of all the man created by the designs of fabrics and fashion through the ages      The problem of research was determined in the absence of a precise understanding of the nature of classical thought in fashion and the absence of a clear perception of the sustainability of this thought in contemporary fashion. He

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Publication Date
Sat Sep 30 2017
Journal Name
College Of Islamic Sciences
Ruling on questioning children by the security authorities: (Comparative Study between Sharia and Law)
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Some of the issues that have become common in our society recently after the Americans entered our country and were rubbed by some security agencies: obtaining some information from children, and the serious consequences that may lead to the lives of innocent people, became common interrogation of some security agencies and rely on their words.
There are significant cases where their testimony needs to be heard, such as their presence in some places where incidents are not witnessed by others, such as schools or being witnesses to certain crimes.
I saw the study of this case in the light of Sharia and law

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Publication Date
Sat Oct 02 2021
Journal Name
International Journal Of Nonlinear Analysis And Applications
Using the wavelet analysis to estimate the nonparametric regression model in the presence of associated errors
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Abstract The wavelet shrink estimator is an attractive technique when estimating the nonparametric regression functions, but it is very sensitive in the case of a correlation in errors. In this research, a polynomial model of low degree was used for the purpose of addressing the boundary problem in the wavelet reduction in addition to using flexible threshold values in the case of Correlation in errors as it deals with those transactions at each level separately, unlike the comprehensive threshold values that deal with all levels simultaneously, as (Visushrink) methods, (False Discovery Rate) method, (Improvement Thresholding) and (Sureshrink method), as the study was conducted on real monthly data represented in the rates of theft crimes f

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Publication Date
Sat Jan 02 2021
Journal Name
The International Journal Of Nonlinear Analysis And Application
Atan regularized for the high dimensional Poisson regression model
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Variable selection in Poisson regression with high dimensional data has been widely used in recent years. we proposed in this paper using a penalty function that depends on a function named a penalty. An Atan estimator was compared with Lasso and adaptive lasso. A simulation and application show that an Atan estimator has the advantage in the estimation of coefficient and variables selection.

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Publication Date
Wed Jan 01 2020
Journal Name
Reviews In Medical Microbiology
Molecular study of some virulence genes of Pseudomonas aeruginosa isolated from different infections in hospitals of Baghdad
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One hundred isolates of Pseudomonas aeruginosa were obtained from patients admitted to Baghdad hospitals, Iraq during the period between May 2018 until July 2018. These isolates were distributed as 15 isolates from blood, 25 isolates from urinary tract infections, 10 isolates from sputum, 12 isolates from wounds, 15 isolates from ear infections, 15 isolates from bronchial wash of patients suffering from respiratory tract infections in addition to 8 isolates from cystic fibrosis patients. The isolates were initially identified by culturing on MacConkey agar, blood agar and P. aeruginosa agar then diagnosed by performing some morphological and biochemical tests. The second diagnosis was done by API 20E system followed by Vitek 2 compact syste

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Publication Date
Sat Sep 16 2023
Journal Name
مجلة الدراسات المستدامة
A Review Article: Use of fertilizers and their gradual release of mineral nutrients as a remedy to this problem have an adverse environmental impact.
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Throughout Agriculture has mostly relied on the use of natural fertilizers throughout human history, which are compounds that increase the nitrogen levels in the soil. Modern agriculture was made possible by the introduction of synthetic fertilizers at the end of the 19th centuryproduction of agriculture. Their application enhanced crop yields and sparked an agricultural revolution unlike anything the world had ever seen.In the near future, synthetic fertilizers are anticipated to continue to have a significant impa ct on human life, both positively and negatively. They are frequently utilized for producing all t ypes of crops and are essential to plant growth. The significance of synthetic fertilizers is their ability to provide the soil w

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