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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
Mon Jan 01 2024
Journal Name
Aip Conference Proceedings
The dynamical behavior of AIDS and HCV infection model with two modes of transmission
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The aim of this paper is to describe an epidemic model when two SI-Type of diseases are transmitted vertically as well as horizontally through one population. The population contains two subclasses: susceptible and infectious, while the infectious are divided into three subgroups: Those infected by AIDS disease, HCV disease, and by both diseases. A nonlinear mathematical model for AIDS and HCV diseases is Suggested and analyzed. Both local and global stability for each feasible equilibrium point are determined theoretically by using the stability theory of differential equations, Routh-Hurwitz and Gershgorin theorem. Moreover, the numerical simulation was carried out on the model parameters in order to determine their impact on the disease

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Publication Date
Sat Jan 01 2011
Journal Name
Journal Of Engineering
PHYSICAL MODEL OF KEROSENE PLUME MIGRATION IN AN UNSATURATED ZONE OF THE SANDY SOIL
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Physical model tests were simulated non-aqueous phase liquid (NAPL) spill in two-dimensional
domain above the water table. Four laboratory experiments were carried out in the sand-filled
tank. The evolution of the plume was observed through the transparent side of this tank and the
contaminant front was traced at appropriate intervals. The materials used in these experiments
were Al-Najaf sand as a porous medium and kerosene as contaminant.
The results of the experiments showed that after kerosene spreading comes to a halt (ceased) in
the homogeneous sand, the bulk of this contaminant is contained within a pancake-shaped lens
situated on top of the capillary fringe.

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Publication Date
Sat Jun 01 2024
Journal Name
Results In Control And Optimization
Impact of wind flow and global warming in the dynamics of prey–predator model
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Publication Date
Mon Jan 01 2024
Journal Name
Iraqi Journal Of Hematology
Provisional diagnosis of clinically significant hemoglobinopathies and decision on suitability for marriage as part of the premarital screening program in Iraq: Iraqi Society of Hematology Guidelines
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Publication Date
Thu Oct 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
The impact of organizational learning in building intellectual capital in public organizations: comparative research between the universities of Baghdad and al-Mustansiriya
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   Organizational learning is one of the most important means of human resource development in organizations, but most of the organizations, especially public ones do not realize the importance of organizational learning enough, and estimated his role accurately in building intellectual capital, the resource competitive importantly for organizations of the third millennium and who suffers is other end of lack of understanding of its meaning and how to prove its presence and measured in public organizations, so there is the need for this research, which aims to investigate the effect of organizational learning its processes (knowledge acquisition, Information transfer, Interpreting the information, Organizational me

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Publication Date
Fri May 01 2020
Journal Name
Journal Of Engineering
Parametric Study on Unconnected Piled Raft Foundation Using Numerical Modelling
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Piled raft is commonly used as foundation for high rise buildings. The design concept of piled raft foundation is to minimize the number of piles, and to utilize the entire bearing capacity. High axial stresses are therefore, concentrated at the region of connection between the piles and raft. Recently, an alternative technique is proposed to disconnect the piles from the raft in a so called unconnected piled raft (UCPR) foundation, in which a compacted soil layer (cushion) beneath the raft, is usually introduced.  The piles of the new system are considered as reinforcement members for the subsoil rather than as structural members. In the current study, the behavior of unconnected piled rafts systems has been studie

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Publication Date
Sun Nov 01 2020
Journal Name
The Iraqi Journal For Information And Documentation Studies
Improving students' cognitive abilities using modern technologies: an experimental study
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The importance of knowledge is represented in the use of various sources of information, the corresponding to the same level of importance is the use of modern means and technologies in the delivery and investment of these sources to the beneficiaries, among these means and technologies are the multimedia that deal with most of the human senses, but the most important of which is sight and hearing, if these are invested the means in the field of education will give many positive results, such as the speed of receiving information, its clarity, and its freedom from impurities and influences, as well as its stability in memory as it is based on nderstanding, not memorization. On this basis, the experience of supporting the education process

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Terramechanics
Interaction of a rigid beam resting on a strong granular layer overlying weak granular soil: Multi-methodological investigations
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In the geotechnical and terramechanical engineering applications, precise understandings are yet to be established on the off-road structures interacting with complex soil profiles. Several theoretical and experimental approaches have been used to measure the ultimate bearing capacity of the layered soil, but with a significant level of differences depending on the failure mechanisms assumed. Furthermore, local displacement fields in layered soils are not yet studied well. Here, the bearing capacity of a dense sand layer overlying loose sand beneath a rigid beam is studied under the plain-strain condition. The study employs using digital particle image velocimetry (DPIV) and finite element method (FEM) simulations. In the FEM, an experiment

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Publication Date
Tue Sep 01 2020
Journal Name
Baghdad Science Journal
In Silico Characterization of a Cyclin Dependent Kinase -A (CDKA) and its Coding Gene in some Oryza Species
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Rice (Oryza sativa) is a fundamental food for the majority of world population. Cyclin Dependent Kinase -A (CDKA) accelerates transition through different stages of cell cycle and contributes in gametes formation. In the present investigation, a CDKA encoding gene along with the corresponding protein were characterized in O. sativa Indica Group, O. glaberrimaO. barthii, O. brachyantha, O. glumipatula, O. longistaminata, O. meridionalis, O. nivara, O. punctata and O. rufipogon using in silico analyses. The results reflected little variation in most species except O. longistaminata and O. brachyantha. Compared with the remaining species, O. longistaminata

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Publication Date
Mon Jan 02 2017
Journal Name
Journal Of Educational And Psychological Researches
The effectiveness of the structural model of learning in the acquisition of geographical concepts among students of the first grade average)
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The current research aims to find out ( the effectiveness of the structural model of learning in the acquisition of geographical concepts at the first grade average students ) , and achieving the goals of research has been formulating the null hypothesis of the following :

    " There is no difference statistically significant when Mistoi (0.5 ) between the mean scores of the collection of students in the experimental group that is studying the general geographical principles " Bonmozj constructivist learning " and the mean scores of the control group , which is considering the same article ," the traditional way " to acquire concepts.

The researcher adopted th

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