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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
Thu Jan 01 2015
Journal Name
Conference Proceedings Of The Society For Experimental Mechanics Series
A comparative study of mode decomposition to relate next-ERA, PCA, and ICA modes
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This paper discusses a comparative study to relate parametric and non-parametric mode decomposition algorithms for response-only data. Three popular mode decomposition algorithms are included in this study: the Eigensystem Realization Algorithm with the Natural Excitation Technique (NExT-ERA) for the parametric algorithm, as well as the Principal Component Analysis (PCA) and the Independent Component Analysis (ICA) for the non-parametric algorithms. A comprehensive parametric study is provided for (i) different response types, (ii) excitation types, (iii) system damping, and (iv) sensor spatial resolution to compare the mode shapes and modal coordinates of using a 10-DOF building model. The mode decomposition results are also compared using

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Publication Date
Wed Mar 29 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
A Comparative Biochemical Study of Proteins Profile in Iraqi Children and Adolescent with ?-Thalassemia
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The aim of the present research is to study different protein fractions in sera of children and adolescent with  β –thalassemia major and minor and to compare the results with that of healthy control.One hundred fifty children and adolescents were enrolled in this study,including 50 patients with β- thalassemia major , 50 patients with  β- thalassemia minor as pathological control group and another apparently 50 healthy individuals as a control group. The age of all studied  groups ranged from (4-18)years.Total protein, albumin and immunoglobulins were estimated in sera of all subjects.  A Significant  decrease  was  found  in  the  total  protein and  albumin&nb

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Publication Date
Thu Jul 08 2021
Journal Name
Turkish Online Journal Of Qualitative Inquiry (tojqi)
Civil Protection of Rights contiguous to Author’s Royalty in Iraqi Law A comparative study
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Publication Date
Sun Oct 01 2017
Journal Name
International Journal Of Oral And Maxillofacial Surgery
Characteristics of mandibular injuries caused by bullets and improvised explosive devices: a comparative study
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The purpose of this study was to investigate the difference in mandibular trauma caused by two mechanisms for the delivery of missile injuries: firearms and improvised explosive devices (IEDs). The data investigated included sex, age, mechanism of injury, and other clinical and radiographic manifestations. Seventy consecutive patients, predominantly male, with a mean age of 28.6 ± 14 years (range 2–60 years) were enrolled: 38 patients (54.3%) sustained mandibular fractures caused by bullet injuries and 32 patients (45.7%) had mandibular fractures caused by IED explosion injuries. The study revealed that the differences in most of the investigated variables were not statistically significant; the only significant differences were the inci

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Publication Date
Fri Jan 01 2021
Journal Name
E3s Web Of Conferences 318, 03002 (2021)
A Comparative Study on Behavior of RC Columns Strengthened by CFRP and Steel Jacket
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This paper studies the behavior of axially loaded RC columns which are confined with carbon fiber reinforced polymers’ sheet (CFRP) and steel jackets (SJ). The study is based on twelve axially loaded RC columns tested up to failure. It is divided into three schemes based on its strengthening type; each scheme has four columns. The main parameters in this study were the compressive strength of the concrete and steel reinforcement ratio. Furthermore, the results of the experimental test showed a substantial enhancement in the column's load-carrying capacity. When compared to the original columns, the CFRP sheet had a significant effect on improving the ductility of the column by increasing the axial deformation by about 59.2 to 95.7

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Publication Date
Thu Dec 30 2021
Journal Name
College Of Islamic Sciences
Non-traded Tales in Imami and Hanafi Doctrines (A Comparative Study of Religion Fundamentals)
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The present study is about tales attributed to certain people and are not traded. Such a study has a great importance for religion scholars and conveyors of hadiths since it is considered as one of the important sources of Islamic legislation that represent the Holy Sunna, and the majority of the recent study is concerned with non-traded tales of religion scholars. The research starts with the definition of such type of tales and then its types, conditions, legality, exceptions, and the benefit from studying such matter. It is mainly concerned with the opinions of the Imami and Hanafi region scholars respectively, and with comparing between the two doctrines i.e. Imami and Hanafi at the end of each

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Publication Date
Mon Jul 01 2013
Journal Name
Political Sciences Journal
The regional attitude towards the change in the Arab region: turkey as a case study
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This research deals with the nature of the Turkish attitude towards the events of the Arab Spring which the Arab region witnessed recently, as this attitude is characterized by hesitation and utter confusion about those events at its beginning. However, the development of events and the consequent repercussions led the Turkish decision makers of the foreign policy to reconsider their attitude towards those events for political, economic, cultural and social motives.

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Publication Date
Sat Aug 01 2015
Journal Name
2015 37th Annual International Conference Of The Ieee Engineering In Medicine And Biology Society (embc)
Tsallis entropy as a biomarker for detection of Alzheimer's disease
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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
Effectiveness of Graduality, Escalation and Argumentation in Quranic Politeness Discourse “Surat Ghafir a Model” A Pragmatic Study
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Theauthor addressed politeness discourse in “Surat Ghafir”. Quran texts include many rhetorical utterances which are considered pragmatic mechanismsconcerned with finding polite discourse. examining these texts allow to determine the effectiveness degree in the discourse, and to find the effect level that leads to interaction between the speaker and the listener. Graduation is considered an effect and a mechanism of discourse escalation.
The author reached a common definition of the graduation effectiveness term, due to its importance in finding polite discourse that is constructed by lingual manifestations some of which are escalation and graduation. Escalation is a mechanism to show the level of discourse graduation, it is a mea

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Publication Date
Thu Apr 01 2021
Journal Name
Iop Conference Series: Earth And Environmental Science
Reality analysis of the state of spatial distribution of green areas using geographic information systems (GIS) – The holy city of Najaf as a case study
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Abstract<p>Green areas are an essential component of city planning, as they serve as an outlet for them to spend their free time, in addition to the environmental role that these green areas play in improving the city’s climate by purifying the air and beautifying the city. The study’s problem is summarized in identifying the appropriateness of the current spatial distribution of green areas in the city of Najaf with the current population densities and the pattern in which green areas are distributed using GIS and knowing the per capita share of those green areas in the city, the research assumes that the inconsistency of spaces between regions Green and residential neighbourhoods need to c</p> ... Show More
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