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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
Mon Dec 30 2019
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Synthesis and Characterization of Nano Y Zeolite Using MWCNT as Media for Crystal Growth
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   The present research was conducted to synthesis Y-Zeolite by sol-gel technique using MWCNT (multiwalled carbon nanotubes) as crystallization medium to get a narrow range of particle size distribution with small average size compared with ordinary methods. The phase pattern, chemical structure, particle size, and surface area were detected by XRD, FTIR, BET and AFM, respectively. Results shown that the average size of Zeolite with and without using MWCNT were (92.39) nm and (55.17) nm respectively .Particle size range reduced from (150-55) nm to (130-30) nm. The surface area enhanced to be (558) m2/g with slightly large pore volume (0.231) km3/g was obtained. Meanwhile, degree of crystallization decrease

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Publication Date
Fri Apr 01 2022
Journal Name
Baghdad Science Journal
Colistin as A Good Monotherapy to Restrain the Pathogenicity of Acinetobacter baumannii In vivo and In vitro
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        Acinetobacter baumannii  (A. baumannii) is a major opportunistic nosocomial pathogen, mostly resistant to several groups of antibiotics. Colistin is now used as a last-line treatment for isolates that are highly resistant. The purpose of this study is to identify the importance of LptD; which is involved in the translocation of LPS from the inner membrane to the outer membrane in compartment with LptA and LptC of A. baumannii and its indispensable role as a virulence factor, and the efficiency of colistin as a monotherapy. In the current research, two isolates of A.baumannii were used, the local isolate HHR1 isolated from urine sample and the global strain ATCC 17904, and three antibiot

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Publication Date
Sun Jan 01 2012
Journal Name
Indian Journal Of Dermatology
Lactic acid as a new therapeutic peeling agent in the treatment of lifa disease (frictional dermal melanosis)
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Publication Date
Mon Mar 13 2017
Journal Name
Journal Of Baghdad College Of Dentistry
Comparative Study of The Amount of Apically Extrusion Of Debris During Root Canal Preparation Using Wave Oneâ„¢, Trushape 3Dâ„¢, Hyflexâ„¢ CM and One Shapeâ„¢ Instrumentation Systems (An In Vitro Study)
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Background: Many types of instruments and techniques are used in the instrumentation of the root canal system. These instruments and techniques may extrude debris beyond the apical foramen and may cause post-instrumentation complications. The aim of this study was to evaluate the amount of apically extruded debris resulted by using 4 types of nickel-titanium instruments (WaveOne, TRUShape 3D conforming files, Hyflex CM, and One Shape files) during endodontic instrumentation. Materials and methods: Forty freshly extracted human mandibular second premolar with straight canals and a single apex were collected for this study. All teeth were cut to similar lengths. Pre-weighted glass vials were used as collecting containers. Samples were randoml

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Publication Date
Mon Mar 01 2010
Journal Name
Basrah Journal Of Science
Hiding Three Images at one image by Using Wavelet Coefficients at Color Image
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Publication Date
Sun Jun 20 2021
Journal Name
Baghdad Science Journal
Wireless Propagation Multipaths using Spectral Clustering and Three-Constraint Affinity Matrix Spectral Clustering
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This study focused on spectral clustering (SC) and three-constraint affinity matrix spectral clustering (3CAM-SC) to determine the number of clusters and the membership of the clusters of the COST 2100 channel model (C2CM) multipath dataset simultaneously. Various multipath clustering approaches solve only the number of clusters without taking into consideration the membership of clusters. The problem of giving only the number of clusters is that there is no assurance that the membership of the multipath clusters is accurate even though the number of clusters is correct. SC and 3CAM-SC aimed to solve this problem by determining the membership of the clusters. The cluster and the cluster count were then computed through the cluster-wise J

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Publication Date
Fri Dec 23 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Plant-derived Molecules for the Treatment of Tuberculosis: A Review
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Synthetic anti-TB drugs are being used to treat tuberculosis (TB) as they are effective, however, they are accompanied by many side effects. The disease has remained largely uncured till date. The use of plant extracts or phytochemicals along with the anti-TB drugs is a very attractive strategy to make the treatment more effective as phytochemicals have no side-effects, are much less toxic than synthetic anti-TB drugs, are safe to use and most importantly, do not produce resistant strains as opposed to synthetic anti-TB drugs. Approximately 420,000 plant species have been identified globally and among them only a few have been explored for their therapeutic potential. Traditional medicine in different parts of the world has employed crud

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Publication Date
Fri Mar 29 2024
Journal Name
مجلة العلوم التربوية والنفسية
Needs in the stories of the Brothers Grimm (a study in content analysis)
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The current study aims to identify the needs in the stories of the Brothers Grimm. The research sample consisted of (3) stories, namely: 1- The story of the Thorn Rose (Sleeping Beauty) 2- The story of Snow White 3- The story of Little Red Riding Hood. The number of pages analyzed reached (15.5) pages, and to achieve the research objectives, Murray's classification of needs was adopted, which contains (36) basic needs that are further divided into (129) sub-needs. The idea was adopted as a unit of analysis and repetition as a unit of enumeration, Reliability was extracted in two ways: 1- Agreement between the researcher and himself over time, where the agreement coefficient reached 97%. The second was agreement between the researcher and tw

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Publication Date
Sun Jun 30 2013
Journal Name
College Of Islamic Sciences
The Greatness of God in Creating the Hoopoe Bird - A Miracle Study - Explanatory
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Praise be to God, Lord of the worlds, and prayers and peace be upon the best of the messengers, Muhammad, and all his family and companions. And after:
For when I had the pleasure of looking at the chapters of the Noble Qur’an, and its evident signs, my view fell on one of its brightest verses, and it is the Almighty saying: ﭽﯜ ﯝ ﯞ ﯟ ﯠ ﯡ ﯢ ﯣ ﯤ ﯥ ﯦ ﯧ ﯨﭼ (). The tag: (God’s Greatness in Creating a Hoopoe). The research methodology required that I divide it into four sections:
The first topic: an overview of birds.
The second topic: the characteristics and characteristics of hoopoe.
The third topic: the logic of the bird.
The fourth topic: Praise the bird.
This has relied in my research on

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Publication Date
Sun Oct 01 2023
Journal Name
Nasq
The Impact of Harold Pinter’s Drama Upon the Iraqi Theatre: A Case Study
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THE IMPACT OF BRITISH THEATER UPON IRAQI DRAMA