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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
Wed Oct 04 2023
Journal Name
History Of Medicine
Theoretical Biological Activities and Docking studies of new amino-acids Derivatives of Oseltamivir for The Treatment of Coronavirus Disease 2019
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Antiviral medications may be the best choices for COVID-19 treatment until particular therapeutic treatments become available. Tamiflu (oseltamivir) is a neuraminidase inhibitor licensed for the management and defense against influenza types A and B. Oseltamivir-based medication combinations are currently being used to treat COVID-19 patients who also have the new coronavirus 1 SARS-CoV-2. 1 Oseltamivir administration was related with a less time spent in the hospital, quicker recovery 1 and discharge, and a decreased mortality rate. Docking is a modern computational method for identifying a hit molecule by assessing the binding ability of molecular medicines within the binding target pocket. In this work, we chose 21 ligand compounds that

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Publication Date
Sat Apr 01 2023
Journal Name
Iop Conference Series: Earth And Environmental Science
Using PCR and Gel Electrophoresis Techniques to Molecular Confirm and Detection for Flowering Gene Presence in Maize Hybrids
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Abstract<p>The laboratory experiment was conducted in the laboratories of the Musayyib Bridge Company for Molecular Analyzes in the year 2021-2022 to study the molecular analysis of the inbreed lines and their hybrids F1 to estimate the genetic variation at the level of DNA shown by the selected pure inbreed lines and the resulting hybrids F1 of the flowering gene. Five pure inbreed lines of maize were selected (ZA17WR) Late, ZM74, Late, ZM19, Early ZM49WZ (Zi17WZ, Late, ZM49W3E) and their resulting hybrids, according to the study objective, from fifteen different inbreed lines with flowering time. The five inbreed lines were planted for four seasons (spring and fall 2019) and (spring and fall 2</p> ... Show More
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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)
Uric Acid as a Natural Scavenger of Peroxynitrite in a Sample of Iraqi Patients with Rheumatoid Arthritis
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Rheumatoid arthritis (RA) is a chronic inflammatory disease associated with decreased antioxidant state .This study aim to investigate the status of oxidant/antioxidant in a sample of  Iraqi patients with RA and the role of peroxynitrite and its natural scavenger uric acid in them .This case-controlled study was conducted at Baghdad teaching hospital /Baghdad from December 2010-May 2011 . Twenty-five patients with mean age 39 years and 25 apparently healthy subject as controls with mean age 29 years were included in the study .Investigations include estimation of serum levels of nitric oxide (NO)  ,peroxynitrite (PN) , malondialdehyde (MDA)  , and uric acid (UA) .Serum PN levels were significantly elevated in RA patients a

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Publication Date
Sat Jan 31 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of Propolis from Kurdistan region as a new resinous sealer in root canal obturation-part I biocompatibility study
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Background: Many materials were proposed as root canal obturating materials but the biocompatibility issue remains to be a critical one. Propolis has been used as a therapeutic agent since the time of Hippocrates. It is known that propolis exhibits some pharmacological activities, such as antibacterial, antiviral, antifungal and anti inflammatory activity. Materials and methods: Eighteen albino rats were used in the study and divided randomly into three groups of 6 animals for each group. Each group was scheduled to be sacrificed at different time periods, which were three days, one week and three weeks. Propolis and ZOE sealer implants of 4mm in diameter and 0.5 gm in weight were implanted in the dorsal side of the rats. At the end of the

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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Engineering
Civilizations and Environmental Particulars of Place in Islamic Holy Thresholds in Iraq (Alkadhumain Holy Threshold as a case study)
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Islamic shrines architecture is one of the Islamic Architectural building types. It is called (Thresholds); (Atabat) in Arabic. Thoroughbred throughout the Islamic world from the east to west. In addition, it carries the style features and peculiarities of uniqueness from the rest of the types of Islamic architecture. By virtue of the particularity of its function as tomb for important person in Islamic history. Islamic shrines architecture has grown and evolved in started from the small shrines, and then taken to widen with the evolution of time in line with the value of the event and the rituals associated with it. Some of them to became centers of large cities of the largest in many parts of the Islamic world.

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Publication Date
Sat Dec 21 2019
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Synthesis, Characterization and Preliminary Anticancer Study of Novel 5-fluorouracil Conjugate with Pyrrolidine Dithiocarbamate as a Mutual Anticancer Prodrug
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 5-Fluorouracil is one of the commonly used chemotherapy drugs in anticancer therapy; unfortunately treatment with 5-FU by solely has many drawbacks  low lipophilicity, low permeability, low molecular weight, and its relatively poor plasma protein binding; also a brief half-life therefore frequent administration is required to maintain the optimal therapeutic plasma level which in addition to its poor selectivity, drug resistance and limited penetration to cancer cells; leads to increased incidence of side-effects to healthy cells/tissues and low response rates. In order to minimize these drawbacks; 5-FU was chemically  conjugated with pyrrolidine dithiocarbamate (PDTC) in a mutual prodrug moiety (S-(9H-purin-6-yl) 3-(

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Publication Date
Mon Apr 04 2022
Journal Name
Journal Of Educational And Psychological Researches
The Degree of Implementation of the Coronavirus Prevention Standards (Covid-19) In the Kingdom Of Saudi Arabia (A COMPARATIVE STUDY BETWEEN FAMILIES OF PEOPLE WITH INTELLECTUAL DISABILITIES AND FAMILIES OF ORDINARY PEOPLE)
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The study aims to identify the degree of implementation of the coronavirus prevention standards (covid-19) in the kingdom of Saudi Arabia and compare it with the families of intellectual disabilities. The study population consisted of all families residing in the Kingdom of Saudi Arabia. To achieve the objectives of the research, the analytical descriptive approach was employed. The study sample consisted of (372) families, among them (84) families with intellectual disabilities, and (288) families without intellectual disabilities. They were chosen from the Saudi community according to what is available for collection in a simple random way, using the standard criteria for the prevention of coronavirus (Covid- 19) Prepared by the resear

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Publication Date
Fri Dec 01 2023
Journal Name
Iop Conference Series: Earth And Environmental Science
A study of the Effect of Diesel Oil Contamination with Glycol on the Performance of a Diesel Engine
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Abstract<p>The performance of a diesel engine was tested with diesel oil contaminated with glycol at the engineering workshop/Department of Agricultural Machines and Equipment / College of the Agricultural Engineering Sciences at the University of Baghdad. To investigate the impact of different concentrations of glycol on the performance of a diesel engine, an experimental water-cooled four-stroke motor was utilized, with oil containing 0, 100, and 200 parts per million (ppm). Specific fuel consumption, thermal efficiency, friction power, and exhaust gas temperature were examined as performance indicators. To compare the significance of the treatments, the study employed a full randomization des</p> ... Show More
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Publication Date
Fri Dec 01 2023
Journal Name
Iop Conference Series: Earth And Environmental Science
A study of the Effect of Diesel Oil Contamination with Glycol on the Performance of a Diesel Engine
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Abstract<p>The performance of a diesel engine was tested with diesel oil contaminated with glycol at the engineering workshop/Department of Agricultural Machines and Equipment / College of the Agricultural Engineering Sciences at the University of Baghdad. To investigate the impact of different concentrations of glycol on the performance of a diesel engine, an experimental water-cooled four-stroke motor was utilized, with oil containing 0, 100, and 200 parts per million (ppm). Specific fuel consumption, thermal efficiency, friction power, and exhaust gas temperature were examined as performance indicators. To compare the significance of the treatments, the study employed a full randomization des</p> ... Show More
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Publication Date
Thu Dec 14 2023
Journal Name
4th International Conference Of Modern Technologies In Agricultural Sciences
A study of the Effect of Diesel Oil Contamination with Glycol on the Performance of a Diesel Engine
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The performance of a diesel engine was tested with diesel oil contaminated with glycol at the engineering workshop/Department of Agricultural Machines and Equipment / College of the Agricultural Engineering Sciences at the University of Baghdad. To investigate the impact of different concentrations of glycol on the performance of a diesel engine, an experimental water-cooled four-stroke motor was utilized, with oil containing 0, 100, and 200 parts per million (ppm). Specific fuel consumption, thermal efficiency, friction power, and exhaust gas temperature were examined as performance indicators. To compare the significance of the treatments, the study employed a full randomization design (CRD), with three replicates for each treatment at th

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