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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 Sep 30 2001
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Determination of Corrosion Parameters for a Cathodic Reaction Complicated by IR Drop Effect in a Flow System
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Publication Date
Sun Aug 24 2025
Journal Name
Journal Of Baghdad College Of Dentistry
The Effects of Different Investment Materials on Dimensional Accuracy and Surface Roughness of Thermosens Maxillary Complete Dentures
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Background: Limited data are available on the dimensional stability and surface roughness of ThermoSens, which is a material used in denture processing. This study aimed to measure the vertical teeth changes and surface roughness of ThermoSens dentures prepared using three different investment materials. Materials and methods: For the dimensional changes test, 30 complete maxillary dentures were prepared using different investment methods: group I, dental stone; group II, silicone putty; and group III, a mixture of dental stone and plaster (ratio, 1:1; n = 10 for each group). Four screws were attached to the dentures: two were attached to the buccal surface of the canine and first molar, and the other two were attached in the flange areas o

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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Craniofacial Surgery
Novel Application of Platelet-Rich Fibrin as a Wound Healing Enhancement in Extraction Sockets of Patients Who Smoke
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Publication Date
Mon Nov 02 2020
Journal Name
International Journal Of Pharmaceutical Research
Evaluation of Serum Adropin Levels in Nonalcoholic Fatty Liver Disease as A Complication of Hypothyroidism In Iraqi Patients
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Publication Date
Sat Sep 28 2024
Journal Name
Journal Of International Dental And Medical Research
Effect of Air–Particle Abrasion of Dentin Surface on Shear Bond Strength of Lithium Disilicate to Dentin Using Three Different Cements
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This study aims to evaluate the influence of the air abrasion of dentin on the shear bond strength of lithium disilicate using three different types of luting cements. Sixty cylindrical specimens were milled from lithium disilicate CAD/CAM blocks (IPSe.max CAD). Sixty sound human maxillary premolar teeth were decoronated to the level of peripheral dentin, then randomly divided into three groups according to the type of luting cement used for the cementation of the lithium disilicate specimens (n = 20); Group A: Glass ionomer cement (Riva Self- Cure); Group B: Adhesive resin cement (Rely X Ultimate); Group C: Self-adhesive resin cement (Rely X U200). Each group was then further subdivided into two subgroups (n=10); Subgroups AI, BI, and CI,

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Publication Date
Mon Dec 26 2016
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
ESTIMATION OF THE CHEMICAL COMPONENTS OF WASTES PRESSED GRAPES A STUDY THE EFFECT OF THERMAL EXTRACTS TRANSACTIONS IN INHIBITING THE GROWT OF MICROORGANISMS.: ESTIMATION OF THE CHEMICAL COMPONENTS OF WASTES PRESSED GRAPES A STUDY THE EFFECT OF THERMAL EXTRACTS TRANSACTIONS IN INHIBITING THE GROWT OF MICROORGANISMS.
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The chemical composition of wastes of pressed grapes and found that the main components of wastes of pressed grapes, represented by the percentage of moisture was 6.47%, and the proportions are 3.71%. Either carbohydrates amounted to 85.77 %, either in fat models using petroleum ether Petroleum ether) was the increase of 0.27%. estimated the percentage of ash in the sampls was 3.78%, either fiber reached 69.47 %,, in addition to the test extracts towards the growth of seven types of bacteria, which included Bacillus subtilis, Bacillus cereus, Bacillus stearothermophilus, Escherishia coli, Staphylococcus aureus, Salmonella typhimurium and Pseudomonas fluorescens and yeast Candida albicans and Kluyveromyces marxianus, ( diffusion method ).

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Publication Date
Sat Sep 02 2017
Journal Name
Journal Of Engineering
Estimation Curve Numbers using GIS and Hec-GeoHMS Model
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Recently, the development and application of the hydrological models based on Geographical Information System (GIS) has increased around the world. One of the most important applications of GIS is mapping the Curve Number (CN) of a catchment. In this research, three softwares, such as an ArcView GIS 9.3 with ArcInfo, Arc Hydro Tool and Geospatial Hydrologic Modeling Extension (Hec-GeoHMS) model for ArcView GIS 9.3, were used to calculate CN of (19210 ha) Salt Creek watershed (SC) which is located in Osage County, Oklahoma, USA. Multi layers were combined and examined using the Environmental Systems Research Institute (ESRI) ArcMap 2009. These layers are soil layer (Soil Survey Geographic SSURGO), 30 m x 30 m resolution of Digital Elevati

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Publication Date
Sun Feb 03 2019
Journal Name
Iraqi Journal Of Physics
Secure communications by chaotic carrier signal using Lorenz model
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In this paper, the generation of a chaotic carrier by Lorenz model
is theoretically studied. The encoding techniques has been used is
chaos masking of sinusoidal signal (massage), an optical chaotic
communications system for different receiver configurations is
evaluated. It is proved that chaotic carriers allow the successful
encoding and decoding of messages. Focusing on the effect of
changing the initial conditions of the states of our dynamical system
e.i changing the values (x, y, z, x1, y1, and z1).

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Publication Date
Mon Jun 01 2020
Journal Name
Journal Of Engineering
The The Use of Copper and Aluminum Electrodes for Energy Production in a Microbial Fuel Cell
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Microbial fuel cell is a device that uses the microorganism metabolism for the production of electricity under specific operating conditions. Double chamber microbial fuel cell was tested for the use of two cheap electrode materials copper and aluminum for the production of electricity under different operating conditions. The investigated conditions were concentration of microorganism (yeast) (0.5- 2 g/l), solutions temperature (33-45 oC) and concentration of glucose as a substrate (1.5- 6 g/l). The results demonstrated that copper electrode exhibit good performance while the performance of aluminum is poor. The electricity is generated with and without the addition of substrate. Addition of glucose substrate

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Publication Date
Thu Jan 02 2020
Journal Name
Journal Of The College Of Languages (jcl)
The newspaper is a field for the use of phraseologism: Газета как сфера использованиея фразеологических единиц
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Idiomatic expressions in Russian journalism make one important borrowed means for making a dialogue with the receiver's intellect in so far as it has the distinct feature of  having clarity and exactness of meaning. The meaning is seen as a shortcut for covering a series of concepts and details so as to arrive at the intended meaning. This is done by stimulating the reader by the use of certain clear idioms. The use of such idioms in a journalistic text is not for a linguistic purpose only, but it is a cultural and social phenomenon reflecting the type of current changes in the society and it aims at discoursing with the reader's mind. This paper is a practi

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