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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 Sep 15 2017
Journal Name
Journal Of Baghdad College Of Dentistry
In Vitro The Effect of Canals Instrumented With Three Rotary Ni-Ti Systems on The Dislocation Resistance of Guttafusion® Versus Single Cone Obturation Technique
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Background: Complete seal of the root canal system following its chemo-mechanical debridement plays a pivotal role for achieving successful endodontic treatment. This can be established by reducing the gaps between the core filling material and root canal wall. Aim: To assess and compare the dislocation resistance of root canals obturated with GuttaFusion® and TotalFill BC sealer versus single cone obturation technique and TotalFill BC sealer after instrumentation of the canals with WaveOne, ProTaper Next and ProTaper Universal system. Material and Method: Sixty extracted human permanent mandibular premolars were conducted in the current study. The teeth were decorated and left the root with 15mm length; the roots were divided randoml

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Publication Date
Thu Feb 13 2025
Journal Name
5th International Conference On Sustainable Engineering Techniques
Hydrochemical characterization and suitability of groundwater for irrigation in a part of Mahmoudiyah district, Baghdad Governorate, Iraq
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Publication Date
Mon Oct 01 2012
Journal Name
Applied Energy
Analysis of thermal and electrical performance of a hybrid (PV/T) air based solar collector for Iraq
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Publication Date
Mon Oct 01 2012
Journal Name
Applied Energy
Analysis of thermal and electrical performance of a hybrid (PV/T) air based solar collector for Iraq
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The electrical and thermal performance of a typical single pass hybrid photovoltaic/thermal (PV/T) air collector is modeled, simulated and analyzed for two selected case studies in Iraq. An improved mathematical thermo-electrical model is derived in terms of design, operating and climatic parameters of the hybrid solar collector to evaluate its important characteristics: collector flow and heat removal factors, PV maximum power point and its temperature coefficient, and overall power and efficiency. Unlike previous PV/T thermal models, the present model is obtained with some additions and corrections in radiation and convection heat coefficients for the top loss and for the air duct with more applicable sky temperature correlation. The well

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Publication Date
Wed Mar 18 2020
Journal Name
Baghdad Science Journal
Synthesis of Six and Seven-membered Heterocyclic Molecules Containing an Adamantyl Fragment and an X-ray Crystal Structure of (E)-N-(adamantan-1-yl)-1-(3-nitrophenyl)methanimine
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       Our work included a synthesis of three new imine derivatives—1,3-thiazinan-4-one, 1,3-oxazinan-6-one and 1,3-oxazepin-4,7-dione—which contained an adamantyl fragment. These were produced via the condensation of the Schiff`s base (E)-N-(adamantan-1-yl)-1-(3-aryl)methanimine with 3-mercaptopropanoic acid; 3-chloropropanoic acid; and maleic, citraconic anhydride, respectively. These new imines were prepared via the condensation of adamantan-1-ylamine and 3-nitro-, 3-bromobenzaldehyde in n-BuOH. We obtained a good yield of products. FTIR, 1H NMR spectroscopy and C.H.N.S analysis were used to diagnostic the products. The molecular structure of (E)-N-(adamantan-1-yl

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Publication Date
Sat Apr 20 2024
Journal Name
International Journal Of Disabilities Sports & Health Sciences
Psychological Toughness and its Relationship to Some Coordination, Physical Abilities and Accuracy of Some Basic Skills Performance Among the Iraqi Junior National Handball Team Players
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The aim of the research is to identify psychological toughness and its relationship to some coordination, physical abilities and accuracy of some basic performance skills among the players of the Iraqi junior national handball team players. The hypothesis is the existence of a correlation between psychological toughness, coordination, physical abilities, and the accuracy of some basic skills performance among the players of the Iraqi junior national handball team players. The descriptive approach in the style of correlational relations used to suit the research problem, as the community was determined by (18) players for the Iraqi junior national handball team players, while the sample was (14) players, and the samp

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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Office managers skills and it's impact on the effectiveness of time management A survey of a sample of departments managers in the institutes and faculties at the middle technical university
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The objective of this study is to highlight the skills of office managers and it's impact on the effectiveness of time management in the institutes and faculties of middle technical university and a group of cognitive and practical aims. The managers skills forms mthe modern trend and the main source to provide organizations with highly skilled managers with distinctive performance and because of the sharp changes in the environment which today's organizations works in it , business organizations generally and managers especially realise the importance of time management and it's role in achieving competitive advantage . The problem of this study raised from this point which reflect the extent of departments managers realisation

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Publication Date
Sun Mar 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
The Influence of x ratio and Annealing Temperatures on Structural and Optical Properties for (CuO)<sub>x</sub>(ZnO)<sub>1-x</sub> Composite Thin Films Prepared by PLD
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Abstract<p>Thin films of (CuO)<sub>x</sub>(ZnO)<sub>1-x</sub> composite were prepared by pulsed laser deposition technique and x ratio of 0≤ x ≤ 0.8 on clean corning glass substrate at room temperatures (RT) and annealed at 373 and 473K. The X-ray diffraction (XRD) analysis indicated that all prepared films have polycrystalline nature and the phase change from ZnO hexagonal wurtzite to CuO monoclinic structure with increasing x ratio. The deposited films were optically characterized by UV-VIS spectroscopy. The optical measurements showed that (CuO)<sub>x</sub>(ZnO)<sub>1-x</sub> films have direct energy gap. The energy band gaps of prepared thin films </p> ... Show More
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Publication Date
Mon Nov 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The correlation between identifying needs and choosing the appropriate productive art for use / primary health care centers as an example
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        The purpose of the study is to identify the need to improve health services in Iraq by determining the efficiency of service in health care centres and working on exploiting limited resources through choosing the most efficient technological art represented by using precast concrete technology to fill the shortfall in the establishment health centres for primary care and to explain the impact of this on saving resources, time, and increasing production efficiency. To achieve this, the quantitative analysis adopted as a methodology in the study by determining the size of the deficit in the infrastructure of health centres for primary care according to the standard of a he

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Publication Date
Wed Jun 01 2022
Journal Name
International Journal Of Early Childhood Special Education
A study of the level of skill self-esteem and some aspects of attention (acute - focus - diversion) and their relationship to the performance of the spiking and serve among young tennis players
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The purpose of this paper is to identifying the level of skill self-esteem of the young tennis players in the Governorate of Baghdad, identifying some aspects of attention (acuteness, concentration, and diversion of attention) among the young tennis players of the Baghdad governorate, and identify the skills of serve and serve spiking in tennis by young tennis players in Baghdad governorate. The researchers used the descriptive approach in the correlative relations style for its suitability and the research problem. the research sample was chosen in a deliberate way from the youth team players in tennis for the Governorate of Baghdad and the participants in the 2021-2022 sports season, whose number is (20) male players and (4) young playe

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