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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 Feb 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
The Influential Relationship of Environmental Analysis Processes in the Organization's Development Strategy An exploratory study of the views of a sample of the leaders of the Iraqi Ministry of Interior
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The study aims at diagnosing the importance of environmental analysis (external, industrial and internal) in the organization's strategy for the development of public organizations. The theoretical problem derived from the existence of a knowledge gap for studies and research that dealt with the variables of the study. Three public organizations were selected as the study society (the Civil Defense Directorate, the Directorate of Nationality, Passports and Residency, the General Traffic Directorate). The sample of the study was a sample of (215) managers (managers, department managers, Analysis of the data and hypothesis testing using the appropriate statistical tools, Pearson, the simple and multiple regression coefficient to te

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Publication Date
Wed Dec 30 2020
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Estimation of Serum CD200 and CD200R1 Levels in a Sample of Iraqi Women with Breast Cancer: Their Role as Diagnostic and Prognostic Markers
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Breast cancer is a disease in which cells in the breast grow out of control. CD200 is a cell surface glycoprotein expressed on many cells, it belongs to the immunoglobulin family (Ig) and have a great role in the regulation of inflammation in autoimmunity. CD200 is the ligand for CD200R1 receptor. To determine if serum level of CD200 and its receptor CD200R1 can be used as a diagnostic and prognostic marker in patients with breast cancer.This case control study was carried out at Oncology Teaching Hospital – Medical city in Baghdad. Six groups were enrolled, four groups were confirmed with breast cancer stage (I, II, III and IV), fifth group (benign) and sixth group was control (healthy individual). Serum is divided to me

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Publication Date
Sun Jan 01 2017
Journal Name
Journal Of Engineering
Two – Dimensional Mathematical Model to Study Erosion Problem of Tigris River Banks at Nu’maniyah
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The high and low water levels in Tigris River threaten the banks of the river. The study area is located on the main stream of Tigris River at Nu’maniyah City and the length of the considered reach is 5.4 km, especially the region from 400 m upstream Nu’maniyah Bridge and downstream of the bridge up to 1250 mwhich increased the risk ofthe problemthat itheading towardsthe streetand causingdanger tonearbyareas.

The aim of this research is to identify the reason of slope collapse and find proper treatments for erosion problem in the river banks with the least cost. The modeling approach consisted of several steps, the first of which  is by using “mini” JET (Jet Erosion Test) d

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Publication Date
Tue Dec 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
The Impact Of Knowledge Innovation On Strategic Empowerment (Comparative Field Research)
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The Innovation Of Knowledge Is An Important And A Key Element In The Progress And Business Excellence Organizations, Therefore Requires Several Elements To Help Create And Implement And Move The Innovation Process Of Knowledge, Including The Strategic Empowerment Associated With The Element Of The Process Of Strategic Momentum Engine Driven Wheel Continuous Dynamic Innovation, And Focused Research Problem By Measuring The Availability Of Strategic Empowerment When Individuals From By Senior Departments And Ways To Help Organizations To Provide Empowerment Commensurate With The Requirements Of Achieving The Goals Of Time And Place Appropriate For The Individual, And The Importance Of Research Stems From The Importance Of The Varia

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Publication Date
Fri Jan 01 2021
Journal Name
International Journal Of Agricultural And Statistical Sciences
ESTIMATED NON-PARAMETRIC AND SEMI-PARAMETRIC MODEL FOR LONGITUDINAL DATA
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Publication Date
Tue Nov 27 2018
Journal Name
The Iraqi Geological Journal
CHRONOSTRATIGRAPHICALLY BASED RESERVOIR MODEL FOR CENOMANIAN CARBONATES, SOUTHEASTERN IRAQ OILFIELDS
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The Cenomanian – Turronian sedimentary succession in the south Iraq oil fields, including Ahmadi, Rumaila, Mishrif and Khasib formations have undergone into high-resolution reservoir-scale genetic sequence stratigraphic analysis. Some oil-wells from Majnoon and West-Qurna oil fields were selected as a representative case for the regional sequence stratigraphic analysis. The south Iraqi Albian – Cenomanian – Turronian succession of 2nd-order depositional super-sequence has been analyzed based on the Arabian Plate chronosequence stratigraphic context, properly distinguished by three main chrono-markers (The maximum flooding surface, MFS-K100 of the upper shale member of Nahr Umr Formation, MFS-K140 of the upper Mishrif carbonate

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Publication Date
Sun Sep 05 2010
Journal Name
Baghdad Science Journal
Statistical Model for Polarization Mode Dispersion in Single Mode Fibers
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As the bit rate of fiber optic transmission systems is increased to more than , the system will suffer from an important random phenomena, which is called polarization mode dispersion. This phenomenon contributes effectively to: increasing pulse width, power decreasing, time jittering, and shape distortion. The time jittering means that the pulse center will shift to left or right. So that, time jittering leads to interference between neighboring pulses. On the other hand, increasing bit period will prevent the possibility of sending high rates. In this paper, an accurate mathematical analysis to increase the rates of transmission, which contain all physical random variables that contribute to determine the transmission rates, is presen

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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Investigate Spectroscopic Experimental and Theoretical Model for Hemoglobin Nanoscale Solution
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In the current study, haemoglobin analytes dissolved in a special buffer (KH2PO4(1M), K2HPO4(1M)) with pH of 7.4 were used to record absorption spectra measurements with a range of concentrations from (10-8 to 10-9) M and an absorption peak of 440nm using Broadband Cavity Enhanced Absorption Spectroscopy (BBCEAS) which is considered a simple, low cost, and robust setup. The principle work of this technique depends on the multiple reflections between the light source, which is represented by the Light Emitting Diode 3 W, and the detector, which is represented by the Avantes spectrophotomer. The optical cavity includes two high reflectivity  ≥99%  dielectric mirrors (dia

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Publication Date
Fri May 01 2020
Journal Name
Journal Of Engineering
Building 1D Mechanical Earth Model for Zubair Oilfield in Iraq
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Many problems were encountered during the drilling operations in Zubair oilfield. Stuckpipe, wellbore instability, breakouts and washouts, which increased the critical limits problems, were observed in many wells in this field, therefore an extra non-productive time added to the total drilling time, which will lead to an extra cost spent. A 1D Mechanical Earth Model (1D MEM) was built to suggest many solutions to such types of problems. An overpressured zone is noticed and an alternative mud weigh window is predicted depending on the results of the 1D MEM. Results of this study are diagnosed and wellbore instability problems are predicted in an efficient way using the 1D MEM. Suitable alternative solutions are presented

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Publication Date
Sun Jun 01 2014
Journal Name
2014 International Conference On Computer And Information Sciences (iccoins)
Proposed conceptual model for E-service quality in Malaysian universities
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