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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 Mar 01 2020
Journal Name
Baghdad Science Journal
Eyewitnesses’ Visual Recollection in Suspect Identification by using Facial Appearance Model
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Facial recognition has been an active field of imaging science. With the recent progresses in computer vision development, it is extensively applied in various areas, especially in law enforcement and security. Human face is a viable biometric that could be effectively used in both identification and verification. Thus far, regardless of a facial model and relevant metrics employed, its main shortcoming is that it requires a facial image, against which comparison is made. Therefore, closed circuit televisions and a facial database are always needed in an operational system. For the last few decades, unfortunately, we have experienced an emergence of asymmetric warfare, where acts of terrorism are often committed in secluded area with no

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Publication Date
Mon May 16 2016
Journal Name
Far East Journal Of Mathematical Sciences (fjms)
MINIMIZING WAITING TIMES USING MULTIPLE FUZZY QUEUEING MODEL WITH SUPPLY PRIORITIES
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Publication Date
Mon Oct 22 2018
Journal Name
Journal Of Economics And Administrative Sciences
Using simulation to compare between parametric and nonparametric transfer function model
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In this paper, The transfer function model in the time series was estimated using different methods, including parametric Represented by the method of the Conditional Likelihood Function, as well as the use of abilities nonparametric are in two methods  local linear regression and cubic smoothing spline method, This research aims to compare those capabilities with the nonlinear transfer function model by using the style of simulation and the study of two models as output variable and one model as input variable in addition t

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Publication Date
Fri Jan 01 2021
Journal Name
Bionatura
STUDY THE TIGRIS RIVER IN SOUTH OF BAGHDAD CITY AND MAY USE IT AS IRRIGATION WATER
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Publication Date
Thu Sep 01 2022
Journal Name
Iraqi Journal Of Physics
Calculation of the Magnetic Dipole and Electric Quadrupole Moments of some Sodium Isotopes using Shell Model with Skyrme Interaction
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         In the present work, the magnetic dipole and electric quadrupole moments for some sodium isotopes have been calculated using the shell model, considering the effect of the two-body effective interactions and the single-particle potentials. These isotopes are; 21Na (3/2+), 23Na (3/2+), 25Na (5/2+), 26Na (3+), 27Na (5/2+), 28Na (1+) and, 29Na (3/2+). The one-body transition density matrix elements (OBDM) have been calculated using the (USDA, USDB, HBUMSD and W) two-body effective interactions carried out in the sd-shell model space. The sd shell model space consists of the active 2s1/2, 1d5/2,

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Publication Date
Wed Feb 23 2022
Journal Name
Iraqi Journal Of Agricultural Sciences
AN ECONOMIC ANALYSIS OF SOME FACTORS AFFECTING IN MARKETING EFFICIENCY OF DRY ONION CROP USING THE TOBIT REGRESSION MODEL
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The study was aimed to evaluate the marketing efficiency of dry Onion crop in Salah al-Deen, as estimate the impact of some quality and quantity factors in the efficiency of marketing process of crop using Tobit regression model. The average marketing efficiency of the research sample was 71.3686%. The marketing margins differed according to the marketing channel followed in marketing the crop. The qualitative and quantitative variables in the model are productivity, family size, distance from the market, educational level. The estimated model revealed that a variable productivity is the most important and influential in marketing efficiency, followed by the variable of the distance between the farm and the market, then the variable

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Publication Date
Wed Feb 23 2022
Journal Name
Iraqi Journal Of Agricultural Sciences
AN ECONOMIC ANALYSIS OF SOME FACTORS AFFECTING IN MARKETING EFFICIENCY OF DRY ONION CROP USING THE TOBIT REGRESSION MODEL
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The study was aimed to evaluate the marketing efficiency of dry Onion crop in Salah al-Deen, as estimate the impact of some quality and quantity factors in the efficiency of marketing process of crop using Tobit regression model. The average marketing efficiency of the research sample was 71.3686%. The marketing margins differed according to the marketing channel followed in marketing the crop. The qualitative and quantitative variables in the model are productivity, family size, distance from the market, educational level. The estimated model revealed that a variable productivity is the most important and influential in marketing efficiency, followed by the variable of the distance between the farm and the market, then the variable

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Publication Date
Tue Aug 30 2016
Journal Name
Mechanical Engineering
The Effect of Different Furrow Depths and Speeds of Machinary Units Using A Locally Assembled Combine Implement on Planting Maize
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Publication Date
Thu Aug 04 2022
Journal Name
Journal Of Nanomaterials
Thermal Management of the Melting Process in a Latent Heat Triplex Tube Storage System Using Different Configurations of Frustum Tubes
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In this study, the energy charging mechanism is mathematically modeled to determine the impact of design modifications on the thermofluidic behavior of a phase change material (PCM) filled in a triplex tube containment geometry. The surface area of the middle tube, where the PCM is placed, is supported by single or multi-internal frustum tubes in vertical triplex tubes to increase the performance of the heating and cooling of the system. In addition to the ordinary straight triplex tubes, three more scenarios are considered: (1) changing the middle tube to the frustum tube, (2) changing the inner tube to the frustum tube, and (3) changing both the internal and central tubes to the frustum tubes. The impact of adopting the tube desig

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Publication Date
Thu Nov 01 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Evaluation of the performance of private hospitals from the point of view of the beneficiaries (A field Study in the private Sector hospitals in Baghdad)
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Objectives: This Paper is an attempt to evaluate the services provided by the private hospitals
and to identify the strength and weakness in
their performance The results can be utilized in stating conclusion and recommendations to improve
and activate the role of private medical sector in society .
Methodology: A questionnaire has be designed for this purpose and distributed to ( 132 ) beneficiaries
mostly from Baghdad private hospitals .
Results: The paper has come out with many important results . Among These are the following :
* these who benefit from services provided by private hospitals believe that the good performance of
such hospital is not due to the medical services alone but also to scientific aspect

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