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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
Tue Mar 01 2016
Journal Name
Journal Of Baghdad College Of Dentistry
A Comparison of the Effectiveness of Reciprocating System with Continuous Rotary Systems in Non-Surgical Endodontic Retreatment (An In vitro study)
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Background: Optimal root canal retreatment was required safe and efficient removal of filling material from root canal. The aim of this in vitro study was to compare the efficacy of reciprocating and continuous motion of four retreatment systems in removal of root canal filling material. Materials and Methods: Forty distal roots of the mandibular first molars teeth were used in this study, these roots were embedded in cold clear acrylic,roots were instrumented using crown down technique and rotary ProTaper systemize Sx to size F2 ,instrumentation were done with copiousirrigation of 2.5% sodium hypochlorite and 17% buffered solution of EDTA was used as final irrigant followed by distilledwater, roots were obturated with AH26 sealer and Prota

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Publication Date
Sat Mar 31 2018
Journal Name
Al-anbar Univrsety Jornal For Law And Political Science
The Civil Liability of Police Officers Arising from Pursuit-Related Damages – A Study in Light of American Law and Case Law
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Since the invention of the automobile, no aspect of American life, including crime and its control, has remained untouched by this far-reaching innovation in transportation. Vehicular "hot pursuit"-when suspects in motor vehicles use excessive speed in attempting to elude the police. Unfortunately, accounts of wild chases across crowded inner city streets, through tree-lined suburban boulevards, and over remote country roads are very real and not merely fictional material created for entertaining television and motion picture audiences. The specter of "hot pursuit," complete with screaming sirens and red or blue flashing lights, has become a recurring fact of modem life.1 So, too, are the mishaps involving police vehicles or the vehicles pu

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Publication Date
Mon Nov 24 2025
Journal Name
Journal Of Baghdad College Of Dentistry
A Comparison of the Effectiveness of Reciprocating System with Continuous Rotary Systems in Non-Surgical Endodontic Retreatment (An In vitro study)
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Background: Optimal root canal retreatment was required safe and efficient removal of filling material from root canal. The aim of this in vitro study was to compare the efficacy of reciprocating and continuous motion of four retreatment systems in removal of root canal filling material. Materials and Methods: Forty distal roots of the mandibular first molars teeth were used in this study, these roots were embedded in cold clear acrylic,roots were instrumented using crown down technique and rotary ProTaper systemize Sx to size F2 ,instrumentation were done with copiousirrigation of 2.5% sodium hypochlorite and 17% buffered solution of EDTA was used as final irrigant followed by distilledwater, roots were obturated with AH26 sealer and Prota

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Publication Date
Mon Jan 01 2024
Journal Name
Journal Of The College Of Languages (jcl)
A study of the phonetic changes of Arabic loanwords in Balochi: بررسی تغییرات آوایی وام واژه های عربی در زبان بلوچی
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 Abstract  Lanɡauaɡes, like humans, need communication and interaction to prosper. One of the ways for a language to flourish is to borrow words from other languages. The southern regions of Iran and the coastal countries of Persian Gulf have had strong cultural relations since old times, with language being a dimension of these relations. With their land being geographically located in the realm of Islamic civilization and being Muslims,  Baloch people have had strong connections with the Arab world and the Arabic language.Thus, many Arabic words have made their ways into Balochi language either directly or indirectly through persian language. Since each language has its own unique sound structure, these loanwords have undergone ph

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Publication Date
Mon Sep 01 2025
Journal Name
The Peerian Journal
The Effect of Environmental Factors on Plant Growth: An Analytical Study of Environmental Variables and Their Physiological Response – A Review Article
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The essay discusses how different environmental factors affect plant growth by explaining how each factor affects the physiological processes within the plant. The essay begins by explaining the effect of temperature on plant growth, as high or low temperatures can significantly affect the rate of photosynthesis and lead to a reduction in water and nutrient absorption. It also discusses the light intensity impacting plants because the more appropriate the light intensity is, the more enhanced the plant's photosynthesis ability, and in the excess or insufficient light condition, the growth can be inhibited. Additionally, the article outlines the effect of water shortage on the plant because this leads to the closure of stomata to avoid water

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Publication Date
Fri Dec 31 2021
Journal Name
Dental And Medical Problems
Effect of the local application of bupivacaine in early pain control following impacted mandibular third molar surgery: A randomized controlled study
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Background: Postoperative pain is one of the main complications following impacted mandibular third molar (IMTM) surgery. Objectives: The aim of this study was to assess the effect of the local application of bupivacaine on reducing early postoperative pain following IMTM surgery. Material and methods: A prospective, single-blinded, randomized controlled study was conducted on 40 patients who had undergone the surgical removal of an IMTM under local anesthesia. In the study group (n = 20), absorbable gelatin sponge (AGS) soaked in 3 mL of 0.5% plain bupivacaine hydrochloride was locally applied in the post-extraction socket. In the control group (n = 20), AGS soaked in 3 mL of normal saline was used. Pain intensity was assessed using a pa

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Publication Date
Mon Jan 02 2017
Journal Name
Al-academy
Producing Bone China with local and manufactured materials as substitutes for the traditional materials
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This research studies the possibility of producing Bone China with available local and geological substitutes and other manufactured ones since it’s traditionally produced by Bone ash, Cornish stone, and China clay, while the substitutes are Kaolin instead of China clay and Feldspar potash instead of Cornish stone. Because of the unavailability of Feldspar in Iraq, it was substituted with the manufactured alternative Feldspar. Bone ash was prepared from cow bones with heating treatments, grinding and sifting. The alternative Feldspar was prepared by chemical analysis of the natural Feldspar potash with local materials that include Dwaikhla Kaolin, Urdhuma Silica sand, Potassium Carbonate, and Sodium Carbonate. The mixture was burned at

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Publication Date
Sat Jun 18 2022
Journal Name
Sciencescholar Publication
Logical reasoning skills according to Piaget's model for chemistry students in the college of education for pure sciences Ibn al-Haytham in
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Abstract---The aim of the current research is to identify the level of logical reasoning skills in chemistry students at the Faculty of Education for Pure Sciences/ Ibn Al-Haytham for the academic year (2021-2022). The differences in their level of skills according to the gender variable (males and females) and the academic stages (first- second - third - fourth). The descriptive approach was adopted because it corresponds to the nature of the research objectives. The research sample consisted of (400 )students selected in a relatively random stratified way. The researcher constructed a logical reasoning test, which includes (6) sub-skills , which is (proportional - probabilistic- synthetic- deductive- logic- variable adjustment). The psych

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Publication Date
Fri Dec 30 2011
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Laminar Free Convection in Three Dimensional Inclined Porous Annulus with Fins on the Inner Cylinder
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An experimental and numerical study was carried out to investigate the heat transfer by natural convection in a three dimensional annulus enclosure filled with porous media (silica sand) between two inclined concentric cylinders with (and without) annular fins attached to the inner cylinder under steady state condition. The experiments were carried out for a range of modified Rayleigh number (0.2 ≤Ra*≤ 11) and extended to Ra*=500 for numerical study and for annulus inclination angle of (δ = 0˚, 30˚, 60˚ and 90˚). The numerical study was to give the governing equation under assumptions that used Darcy law and Boussinesq’s approximation and then it was solved numerically using finite difference approximation. It was found that t

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Publication Date
Fri Sep 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
The role of GRI standards in reporting the dimensions of sustainable development - An applied study in a number of local companies on the Iraq Stock Exchange
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The current research aims to shed light on the Global Reporting Initiative (GRI), which helps to report financial and non-financial information by economic units in general and listed on the Iraq Stock Exchange in particular. The research was based on a main premise that apply the criteria of the Global Reporting Initiative (GRI) would provide useful information to users to help them make appropriate decisions. To achieve the goal of the research, the descriptive analysis method was used, and quantitative analysis was used. At the level of the descriptive analysis method, a desk survey was conducted. As for the quantitative analysis, it relied on applied data through a questionnaire form (Questioners) as a research tool, and the

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