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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 Jan 01 2022
Journal Name
Journal Of Stomatology
Preferences of treatments and materials used in the management of exposed pulps: a web-based questionnaire study
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Publication Date
Sun Jul 02 2017
Journal Name
Journal Of Educational And Psychological Researches
Teaching Using Adey- Shire Model and its Effect in Achievement and Critical Thinking for first intermediate students in Mathematics
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The aim of this research is to measure the effect of Adey- Shire model in the achievement and critical thinking of first intermediate female students in mathematics. The researcher adopted the experimental method with a post-test, the research of sample consists of (60) female students, divided into two groups with (30) students in the experimental group, that studied with Adey- Shire model, and (30) students in the control group who studied in the usual way. The two groups are equivalent in many variables. The researcher makes two tests of multiple choices, the first one is an achievement test consists (30) items and another test was for a critical thinking test with (25) items. The statistical analysis make to both tests is made with s

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Publication Date
Sun Nov 23 2025
Journal Name
Sciences Journal Of Physical Education
The impact of a proposal for the curriculum dictated by some of the barriers to the development of motor skills
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The impact of a proposal for the curriculum dictated by some of the barriers to the development of motor skillsA. M. D. Huda Ibrahim RezoukiM. M. Susan Salim DawoodIs the childhood of the most important and most fertile stage of basic education because of their significant impact in building a base on which the stated origin of sound in the early stages older age because the baby at this stage be very vulnerability to environmental factors different surroundings in which to leave their mark on his life in the stages of life other.The Gymnastics of sports long-term training, which begins between the ages very early relative to the rest of other games to reach the stage of the tournament from the age of 13-17 years almost to the women, this a

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Publication Date
Fri Apr 01 2016
Journal Name
Al–bahith Al–a'alami
Journalism of Paper Newspapers in Light of the Competition of the Electronic Press / (A Field Study of Yemeni Daily Newspapers)
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The researcher seeks to get scientific facts through knowing the relationship between the priorities of Yemeni audience in follow-up paper daily newspapers compared to surfing publics the online journalism sites and the nature of information obtained from online journalism sites and printed paper newspapers and the impact of the daily newspapers in the priority of issues and political events among a sample of a group of Yemeni readers in order to identify the extent to keep up the paper daily newspapers of the development in the field of online journalism and the extent of reading paper newspapers under the intense competition by online journalism sites, and are paper newspapers able to keep pace with the actual developments provided by

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Publication Date
Mon Jun 19 2023
Journal Name
Journal Of Engineering
A STUDY OF THE EFFECT OF SEMI-ANGLE OF CONE ON THE VIBRATION CHARACTERISTICS OF CYLINDRICAL-CONICAL COUPLED SHELL STRUCTURE
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In this work, the effect of variation of semi-angle of the conical part on the vibration characteristics of cylindrical-conical coupled structure is investigated. The shell is made of polyester resin reinforced by continuous E-glass fibers. The case is analyzed experimentally and numerically for orthotropic shell structures. The experimental program is conducted by exciting the fabricated structure by an impact hammer and monitoring the response using an attached accelerometer for different semi-angles of the conical part.
Software named SIGVIEW is used to perform the signal processing on the acquired signal in order to measure the natural frequencies and the corresponding mode shapes. The numerical investigation is achieved using ANS

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Publication Date
Thu May 05 2016
Journal Name
International Journal Of Science And Research (ijsr)
Synthesis, Characterization and Antimicrobial Activity Studies of Mixed-1,10-phenanthroline-Mn(II),Co(II), Cu(II), Ni(II) and Hg(II) Complexes with Schiff Base[2,2'-(1Z,1'Z)-(biphenyl-4,4'-diylbis(azan-1-yl-1-ylidene))bis(methan-1-yl-1-ylidene)diphenol]
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Publication Date
Sat May 07 2016
Journal Name
International Journal Of Science And Research
Synthesis, Characterization and Antimicrobial Activity Studies of Mixed-1,10-phenanthroline- Mn(II),Co(II), Cu(II), Ni(II) and Hg(II) Complexes with Schiff Base[2,2'-(1Z,1'Z)-(biphenyl-4,4'- diylbis(azan-1-yl-1-ylidene))bis(methan-1-yl-1- ylidene)diphenol]
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Abstract: The M(II) complexes [M2(phen)2(L)(H2O)2Cl2] in (2:1:2 (M:L:phen) molar ratio, (where M(II) =Mn(II), Co(II), Cu(II), Ni(II) and Hg(II), phen = 1,10-phenanthroline; L = 2,2'-(1Z,1'Z)-(biphenyl-4,4'-diylbis(azan-1-yl-1-ylidene))bis(methan-1-yl-1- ylidene)diphenol] were synthesized. The mixed complexes have been prepared and characterized using 1H and13C NMR, UV/Visible, FTIR spectra methods and elemental microanalysis, as well as magnetic susceptibility and conductivity measurements. The metal complexes were tested in vitro against three types of pathogenic bacteria microorganisms: Staphylococcus aurous, Escherichia coli, Bacillussubtilis and Pseudomonasaeroginosa to assess their antimicrobial properties. From this study shows that a

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Publication Date
Thu Apr 18 2019
Journal Name
Al-kindy College Medical Journal
Immunohistochemical Targeting of p110β Isoform of phosphatidylinositol 3-kinase co-associated with Cyclin-Dependent Kinase 1 in a Group of Tissues from Iraqi Patients with Breast Cancer
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Background: While two-thirds of breast cancers express hormone receptors for either estrogen (ER) and/or progesterone (PR) , genetically altered PI3K pathway was found in more than 70% of ER-positive breast cancers.An aberrant activity of cyclin-dependent kinase 1 (CDK1) in a wide variety of human cancers has selectively constituted an attractive pharmacological targets in MYC-dependent human breast cancer cells.

Aim of the study:  Role of p110-beta as well as and CDK 1  in the pathogenesis of subset of breast cancers and contribution in their carcinogenesis.

Type of the study: is a retrospective study

Methods: This retr

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Publication Date
Mon May 01 2023
Journal Name
Chemical Engineering Research And Design
Treatment of petroleum refinery wastewater by electrofenton process using a low cost porous graphite air-diffusion cathode with a novel design
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Publication Date
Thu Mar 31 2022
Journal Name
Journal Of The College Of Education For Women
Evaluating Teacher Preparation Programs in Scientific Disciplines at the Faculty of Education in Al-Aqsa University in Light of the Requirements of the Labor Market
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The current study seeks to evaluate teacher preparation programs in the scientific disciplines at the College of Education in Al-Aqsa University in the light of the requirements of the labor market. It further aims to reveal the significance of the differences in the sample members’ response averages of to the availability of labor market requirements in the program that prepares the teacher of scientific disciplines at the Faculty of Education in Al-Aqsa University taking into account the (gender, program) variables. The study followed the descriptive analytical approach, and so a questionnaire was distributed to a sample of scientific discipline students in the teacher preparation program adopted in Al-Aqsa University, (200) male and

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