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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 May 15 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Shear bond strength of different lingual buttons bonded to wet and dry enamel surfaces with resin modified glass ionomer cement (in vitro comparative study)
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Background: This study was aimed to investigate the effect of three lingual button (Nickel free / rectangular base, Nickel free / round base and Composite) and bonding environment, wet and dry enamel surface, on: the shear bond strength (SBS) of light and self-cured Resin Modified Glass Ionomer Cements, and the debonding failure sites. Materials and method: One hundred twenty no-carious, free of cracks maxillary first premolar teeth were selected. Three types of orthodontic lingual buttons were used in this study: Nickel free / rectangular base, Nickel free / round base and Composite buttons. The teeth were divided into two groups of sixty teeth each. One group was used for testing the chemically cured GC Fuji Ortho Resin modified Glass Io

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Publication Date
Tue Sep 08 2020
Journal Name
Baghdad Science Journal
Radiological Impact Assessment of Farm Soils and Ofada rice (Oryza sativa japonica) from Three Areas in Nigeria
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Oryza sativa japonica (ofada rice) is largely grown in Aramoko, Abakaliki and Ofada are communities and consumed by both the poor and rich in Nigeria. A total of twenty ofada rice farmlands were identified in each study area and rice samples were randomly collected, thoroughly mixed to make a representative sample from each farmland. Soil samples were collected in each farm to a depth of 5-15cm from at least eight different points and thoroughly mixed together to form a representative sample. The samples were thereafter taken to the laboratory for preparation and spectroscopic analysis. A well-calibrated NaI(Tl) gamma-ray detector was used in spectrometric analysis of the samples and descriptive statistics was used to analyze th

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Publication Date
Fri Apr 19 2019
Journal Name
Plant Archives
NEW INTERESTING RECORDS OF THREE SPECIES FROM PEZIZACEAE AND PYRONEMATACEAE FAMILIES (PEZIZALEA, ASCOMYCOTA) TO KURDISTAN REGION – IRAQ
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The survey was carried out From January to April of 2018 on macrofungi samples collected from different places in Halabja province located in north eastern parts of Iraq-Kurdistan region. This region is rich in forest trees and pasture lands with diversity of shrubs and herbs and is expected to support the growth of several macro fungal species. However, this part of Kurdistan in Iraq is still unexplored from macrofungal point of view. In this paper three species from Pezizaceae and Pyronemataceae families that belonging to (Pezizales, Ascomycota), were reported from Iraqi Kurdistan. These macrofungal species are recorded for the first time from Iraq. Also the species were identified and showing their locations distributed on a map prepared

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Publication Date
Thu Jun 30 2022
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
EFFECT OF SPRAYING ORGANIC EMULSION (APPETIZER) AND NANO NPK WITH UREA ON SOME GROWTH CHARACTERISTICS OF THREE SYNTHETIC CULTIVARS OF MAIZE: EFFECT OF SPRAYING ORGANIC EMULSION (APPETIZER) AND NANO NPK WITH UREA ON SOME GROWTH CHARACTERISTICS OF THREE SYNTHETIC CULTIVARS OF MAIZE
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A field experiment was carried out at the research station of the College of Agriculture - Wasit University / Kut, during the fall season 2021 in soil with texture (sandy mixture) using the RCBD design in the arrangement of splintered plates and with three replications, to study the effect of spraying different combinations of organic emulsion (Appetizer) and NPK nano fertilizer with urea fertilizer on the growth of synthetic cultivars of yellow corn. The main panels included three synthetic varieties of yellow corn (Fajr1, Sumer and Baghdad3), which symbolized by (V1,V2,V3) in sequence, while the secondary panels included five fertilization treatments in which mineral fertilizer (urea) was used 46% nitrogen with the full recomme

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Publication Date
Tue Apr 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
Relationship between Emotional Intelligence and Decision Making Styles And their effect on Performance Excellence the university" An exploratory search for a sample of the administrative leaderships in the Mustansiriya University"
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   Addressed this research the impact of intelligence emotional dimensions of the main(self awareness, and self-management, and social awareness, and relationship management) in the performance excellence the university(performance optimization, and strategic development) this is by middling the styles decision making which are (rational and intuitive, and dependent, and spontaneous, and avoidant), and Go search of an intellectual dilemma raise fundamental questions revolve around the search was to answer those questions through a theoretical framework for search variables first and test models of the relationship and second through the impact six hypotheses President.The objective of the research to make sure the contr

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Publication Date
Tue Nov 09 2021
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The role of integration between the earned value management model and the value flow map in rationalizing the costs of construction projects: applied research in Al-Rasheed General Company for Construction Contracting
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The research problem is that most of the construction projects exceed the planned value, due to the failure to implement the plans on time. The current study aims to monitor the implementation of the project and for each of the executed tasks of the table of quantities in order to detect deviations at the time they occur, evaluate the time and cost performance, and then identify the areas of waste and analyze the implementation of each task in order to diagnose the underlying problems and find possible and applicable solutions in the environment Iraqi. The research was applied in one of the companies specialized in the field of construction projects, and one of the most important conclusions reached is the possibility of applying

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Publication Date
Wed Feb 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Use some of the quality tools to improve the health service: Comparative research between Baghdad's and Yarmouk hospital educational
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Abstract

This research aims to improve the provided health service level inside Baghdad hospitals and the Yarmouk educational, as well as to shed light on the reality of the health service and the quality within the major operations room in both hospitals, as the operations room represent the research community, as was the use of some quality tools Pareto and Ishikawa diagram to measure and assess the level of quality provided, and include research problem to find out what are the problems and obstacles facing the process of improving quality in both hospitals, and whether there are scientifically accurate method to assess the quality of health service in Baghdad's Yarmouk hospital and educational . Where the researcher h

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Publication Date
Sun Oct 01 2017
Journal Name
Agriculture (pol'nohospodárstvo)
Molecular detection of ‘<i>Candidatus</i> Phytoplasma australasia’ and ‘<i>Ca.</i> P. cynodontis’ in Iraq
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Abstract<p>The association of phytoplasma was investigated in symptomatic tomato (<italic>Solanum lycopersicum</italic> L.), eggplant (<italic>Solanum melongen</italic> L.), mallow (<italic>Malva</italic> spp.) and Bermuda grass (<italic>Cynodon dactylon</italic> L.) plants exhibiting witches’ broom and white leaf diseases, respectively. Total DNA was extracted from tomato (n=3), eggplant (n=2), mallow (n=2) and Bermuda grass (n=8) samples. Direct polymerase chain reaction (PCR) was performed using P1/P7 primer set, then PCR products were sequenced. Sequences obtained from tomato, eggplant and mallow shared 99% maximum nucleotide identity with phytoplasm</p> ... Show More
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Publication Date
Fri Jun 16 2023
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Formulation and Assessment of Delayed/Slow-Release Diclofenac Sodium Edible Organogel Utilizing Low Molecular Weight Organogelators
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Organogel as a system was to estimate its capacity to delay and slow the drug release in the duodenum. The gelators, 12HSA (12-hydroxystearic acid), span 60. span 40 were used; the castor oil (CO) and anise oil (AO) also represented the liquid phase. To achieve the goal of this work was by using diclofenac sodium (DS). Organogels specifications were by estimating thermal attitude using tabletop rheology and differential scanning calorimetry (DSC). The organogel strength study was by applying oscillatory rheology tests the amplitude sweep and the frequency sweep. Realizing the morphology of the organogel was done utilizing an optical microscope. CO and AO binding capacity was also manifested. The transition temperatures for all organogels

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Publication Date
Sun Jan 01 2023
Journal Name
Iraqi Journal Of Biotechnology
Molecular Detection of Candida spp. Isolated from Female Patients Infected with COVID-19 in Baghdad City
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Abstract: Coronavirus disease 2019 (COVID-19) is an infectious disease with severe acute respiratory syndrome and first recognized in Wuhan, China, and it has since spread to the world, resulting in the coronavirus pandemic to 2020. The present study aimed to evaluate Molecular study of some types of vaginal fungi isolated from recovered women from Covid-19 in Baghdad governorate. The study was conducted on 213 samples collected between December 2021 and March 2022, where the number of positive samples reached 188 with percentage 88.26%, while the number of negative samples reached 25 with percentage 11.73% by taking vaginal swabs from various female patients in Al- Kadhimiya Teaching Hospital. Three of Candida spp. were isolated: Candida a

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