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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
Sat Mar 30 2019
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Estimation of rock strength from sonic log for Buzurgan oil field: A Comparison study
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It is very difficult to obtain the value of a rock strength along the wellbore.  The value of Rock strength utilizing to perform different analysis, for example, preventing failure of the wellbore, deciding a completion design and, control the production of sand.  In this study, utilizing sonic log data from (Bu-50) and (BU-47) wells at Buzurgan oil field.  Five formations have been studied (Mishrif, Sadia, Middle lower Kirkuk, Upper Kirkuk, and Jaddala) Firstly, calculated unconfined compressive strength (UCS) for each formation, using a sonic log method.  Then, the derived confined compressive rock strengthens from (UCS) by entering the effect of bore and hydrostatic pressure for each formation.  Evaluations th

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Publication Date
Fri Oct 02 2020
Journal Name
International Journal Of Pharmaceutical Research
A turbidimetric method for the quantitative determination of cyproheptadine hydrochloride in tablets using an optoelectronic detector based on the LEDs array
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Publication Date
Fri Oct 02 2020
Journal Name
International Journal Of Pharmaceutical Research
A turbidimetric method for the quantitative determination of cyproheptadine hydrochloride in tablets using an optoelectronic detector based on the LEDs array
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Publication Date
Thu Jul 01 2010
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
SEDIMENTO LOGICAL STUDY OF SHIRANISH FORMATION WELL DD-1 (N-IRAQ)
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Shiranish formation has been divided into two microfacies units: 1-Marly biowacke stone facies 2-Biogenic pack stone facies These microfacies reflected marine deep shelf margin in the upper part of the formation, the lower part was deeper. 238 slides were investigated depending on Mineralogical, compositional and Biological processes, which reflect deep shelf margin at upper part of the formation, but at the lower part open sea environment. The age of the formation is estimated depending on the recognized biostratigraphic zone using the index fossils to be Upper- Middle Maestrichtian.

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Publication Date
Sun Jan 01 2023
Journal Name
International Conference On Scientific Research & Innovation (icsri 2022)
Saccharomyces Cerevisiae as a human pathogen in renal transplant recipients
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Publication Date
Sun Sep 06 2015
Journal Name
Baghdad Science Journal
Methionine as a Spacer between Poly Acrylic acid and Ampicillin
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In this work a novel drug delivery system through modification of poly acrylic acid with Methionine as a spacer between the poly acrylic acid which was converted to its acyl chloride and reacted with Methionine as spacer unit which has been reacted with Ampicillin drug. In vitro drug release study had been conducted successfully in basic medium in pH 7.4 and acidic medium in pH 1.1 at 37?. Due to many problems associated with drug release and, this modification could decrease the side effect of drug. The prepared prodrug polymer was characterized by spectra method [FTIR and 1H?NMR]. Physical properties and intrinsic viscosity of drug polymer were determined. The good results were obtained in the presence of spacer unit with compar

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Publication Date
Fri Apr 01 2016
Journal Name
Journal Of Engineering
Adding Cellulosic Ash to Composting Mix as a Soil Amendment
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Solid waste generation and composition in Baghdad is typically affected by population growth, urbanization, improved economic conditions, changes in lifestyles and social and cultural habits.

A burning chamber was installed to burn cellulosic waste only. It was found that combustion reduced the original volume and weight of cellulosic waste by 97.4% and 85% respectively.

A batch composting study was performed to evaluate the feasibility of co-composting organic food waste with the cellulosic bottom ash in three different weight ratios (w/w) [95/5, 75/25, 50/50].

The composters were kept in controlled aerobic conditions for 7 days. Temperature, moisture, and pH were measured hourly as process succe

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Publication Date
Tue Jan 01 2019
Journal Name
The Turkish Journal Of Endocrinology And Metabolism
Cell-free DNA as a Clinical Indicator in Maternal Blood
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As many expensive and invasive procedures are used for the diagnosis or follow-up of clinical conditions, the measurement of cell-free DNA is a promising, noninvasive method, which considers using blood, follicular fluid, or seminal fluid. This method is used to determine chromosomal abnormalities, genetic disorders, and indicators of some diseases such as polycystic ovary syndrome, pre-eclampsia, and some malignancies. Cell-free DNA, which are DNA fragments outside the nucleus, originates from an apoptotic process. However, to be used as a marker for the previously mentioned diseases is still under investigation. We discuss some aspects of using cell-free DNA measurements as an indicator or marker for pathological conditions.

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Publication Date
Sat Dec 01 2018
Journal Name
Political Sciences Journal
political culture as a tool to analyse Decentralization Experience in
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It sheds light on the cultural dimension in the decentralized administration experience in Iraq as evaluation tool by adding a new dimension in studying decentralization in addition to the administrative, political and legal dimensions .The proposal of study is that without the civil political culture ,the administrative decentralization in Iraq which remains weak and it may be imposed to a set of problems. - The study includes an introduction, conclusion and a set of political and cultural issues , its components and it may have the political analysis of this culture and its role in determining the movement of the administrative decentralized movement in Iraq post 2003.

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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Use A State Space Model and Forecast House Prices in Baghdad.
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The purchase of a home and access to housing is one of the most important requirements for the life of the individual and the stability of living and the development of the prices of houses in general and in Baghdad in particular affected by several factors, including the basic area of the house, the age of the house, the neighborhood in which the housing is available and the basic services, Where the statistical model SSM model was used to model house prices over a period of time from 2000 to 2018 and forecast until 2025 The research is concerned with enhancing the importance of this model and describing it as a standard and important compared to the models used in the analysis of time series after obtaining the

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