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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 Oct 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The reflection of strategic knowledge management on an improvement of excellent performance: A survey study at the Institution of Industrial Development and Research- the Ministry of Iraqi Industry (IDRMII)
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The current study aims to investigate the effect of strategic knowledge management practices on an excellent performance at the Institution of Industrial Development and Research- the Ministry of Iraqi Industry (IDRMII). The present research is designed according to the descriptive method. To achieve the mentioned research objective, the researchers used the questionnaire as the main data collection tool. The research sample was 150 managers who are working at the top and middle management levels. To analyses the data gathered and reaching the results, several statistical techniques were used within AMOS.V25, SPSS.V21Software, This study reached a set of results, the most important of which is the existence of a positive correlat

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Publication Date
Sun Jan 01 2023
Journal Name
Aip Conference Proceedings
Design and establishment of an implementation program to simulate the far field propagation for a Gaussian beam of x-ray laser
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Publication Date
Sat Dec 02 2017
Journal Name
Al-khwarizmi Engineering Journal
Design of a Programmable System for Failure Modes and Effect Analysis of Steam-Power Plant Based on the Fault Tree Analysis
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In this paper, the system of the power plant has been investigated as a special type of industrial systems, which has a significant role in improving societies since the electrical energy has entered all kinds of industries, and it is considered as the artery of modern life.

   The aim of this research is to construct a programming system, which could be used to identify the most important failure modes that are occur in a steam type of power plants. Also the effects and reasons of each failure mode could be analyzed through the usage of this programming system reaching to the basic events (main reasons) that causing each failure mode. The construction of this system for FMEA is dependi

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Publication Date
Sun Mar 01 2020
Journal Name
Sustainable Chemistry And Pharmacy
A sustainable approach to utilize olive pips for the sorption of lead ions: Numerical modeling with aid of artificial neural network
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Publication Date
Tue Jun 03 2025
Journal Name
Journal Of Biotechnology Research Center
The Link between NAFLD and Colorectal Cancer: Insights from Liver Function Enzymes and Serum Biomarkers in a Case-Control Study
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Background: Colorectal cancer (CRC) is a major killer, and nonalcoholic fatty liver disease (NAFLD) affects almost one-quarter of the global population. The aim of the study is to Investigate the correlation between nonalcoholic fatty liver disease (NAFLD) and an increased risk of colorectal cancer (CRC), as well as the relationship between liver function enzymes and specific serum biomarkers in CRC patients with NAFLD. Methods: A case-control study involving 60 participants was conducted from February to August 2022. The patients with colon cancer were examined at Baghdad Medical City's Al-Amal Hospital for Radiation and Nuclear Medicine and Oncology Teaching Hospital, and blood samples were taken. Thirty patients with NAFLD who ha

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Publication Date
Tue Sep 28 2021
Journal Name
Journal Of The College Of Education For Women
Classism Hate Speech in Katherine Mansfield's Short Story ‘The Doll’s House’: A Pragmatic Study: ايمان نوري جاسم , مصلح شويش احمد
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Hate speech (henceforth HS) has recently spread and become an important issue. This type of speech in children's writings has a particular formulation and specific objectives that the authors intend to convey. Thus, the study aims at examining qualitatively and quantitatively the classism HS and its pragmatic functions via identifying the speech acts used to express  classism HS, the implicature instigated as well as impoliteness. Since pragmatics is the study of language in context, which is greatly related to the situations and speaker’s intention, this study depends on pragmatic theoriespeech acts, impoliteness and conversational implicature) to analyze the data which are taken from Katherine Mansfield's short story (The D

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Publication Date
Mon Jun 30 2025
Journal Name
Babcock University Medical Journal
Microbial Diversity and Antibiotic Resistance Patterns in Burn and Wound Infections: A Study from the Al-Kindy Teaching Hospital, Iraq
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Objective: Comprehending microbial diversity and antibiotic resistance patterns is essential for efficient treatment protocols. This study sought to determine the incidence of bacterial and fungal pathogens responsible for burn and wound infections and their antibiotic susceptibility profiles. Methods: This cross-sectional study involved 140 patients with burn or wound infections. Sterile swabs and pus aspiration were employed to collect samples, which were subsequently processed using standard microbiological procedures. Antibiotic resistance was determined using the Kirby-Bauer disc diffusion method, following Clinical and Laboratory Standards Institute (CLSI) guidelines. Data was analysed using IBM SPSS version 25.0, and the Chi-

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Publication Date
Tue Dec 19 2023
Journal Name
Bulletin Of The Iraq Natural History Museum
MORPHOLOGICAL AND MOLECULAR STUDIES OF KAIS KINGFISH CYPRINION KAIS HECKEL, 1843 (PISCIES, CYPRINIFORMES, CYPRINIDAE) FROM THE MIDDLE OF IRAQ
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Cyprinidae species are the most abundant and widely distributed fish species in the inland waters of Iraq. Cyprinids are complex species, and it is difficult to identify them on the basis of morphology. Thus, the morphological characteristics must be achieved and confirmed by molecular analysis. Twenty specimens of Cyprinion kais Heckel, 1843 (Piscies, Cypriniformes, Cyprinidae) were collected from two localities at Tigris River in the middle of Iraq: five specimens from Al-Tharthar Lake, Saladin Province, and 15 specimens from Al- Zubaydiyah sub-district, Wasit Province. The DNA sequences of C. kais were done using the mitochondrial DNA cytochrome b (cytb) gene. After analysis, the sequences were compared with sequences of ot

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Publication Date
Sun Oct 01 2023
Journal Name
Baghdad Science Journal
Molecular detection by some virulence genes of Salmonella enterica subsp. enterica isolated from the stool of children with diarrhea
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Diarrhea is a real disease in childhood which could cause death. Therefore, this study was conducted to isolate Salmonella from 350 stool samples taken from children under five years in age, suffering from diarrhea during the period from March 2019 to March 2020 in Tikrit city / Iraq. The results showed the possibility to isolate ten isolates of Salmonella enterica subsp. Enterica, an infection rate, represents 2.875% of the total rate of patients who suffer from diarrhea. The virulence genes were investigated for ten isolates of S. enterica subsp. enterica, the result is that all isolates possessed the genes stn, invA, lpfA with an appearance percentage of 100%, whi

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Publication Date
Sat Dec 02 2023
Journal Name
Bulletin Of The Iraq Natural History Museum
MORPHOLOGICAL AND MOLECULAR STUDIES OF KAIS KINGFISH CYPRINION KAIS HECKEL, 1843 (PISCIES, CYPRINIFORMES, CYPRINIDAE) FROM THE MIDDLE OF IRAQ
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Cyprinidae species are the most abundant and widely distributed fish species in the inland waters of Iraq. Cyprinids are complex species, and it is difficult to identify them on the basis of morphology. Thus, the morphological characteristics must be achieved and confirmed by molecular analysis. Twenty specimens of Cyprinion kais Heckel, 1843 (Piscies, Cypriniformes, Cyprinidae) were collected from two localities at Tigris River in the middle of Iraq: five specimens from Al-Tharthar Lake, Saladin Province, and 15 specimens from Al- Zubaydiyah sub-district, Wasit Province

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