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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 Jan 02 2019
Journal Name
Journal Of Global Pharma Technology
Nanocrystal Technology as a Tool for Improving Dissolution of Poorly Soluble Drugs
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Many approaches have been developed over time to counter the bioavailability limitations of poorly soluble drugs. With advances in nanotechnology in recent decades, this issue has been approached through the formulation of drugs as nanocrystals. Nanocrystals consist of pure drug(s) and a minimum of surface active agent(s) required for stabilization. They are carrier-free submicron colloidal drug delivery systems with a mean particle size typically in the range of 200 - 500 nm. By reducing particle size to nanoscale, the surface area available for dissolution is increased, and thus bioavailability is enhanced. Drug nanocrystals constitute a versatile formulation approach to enhance the pharmacokinetic and pharmacodynamic properties of poorly

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Publication Date
Sun Jun 21 2020
Journal Name
Baghdad Science Journal
Synthesis of Carbon Nano Rods from Plastic Waste (PP) Using MgO AS A Catalyst
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    In this research, CNRs have been synthesized using pyrolysis of plastic waste(pp) at 1000 ° C for one hour in a closed reactor made from stainless steel, using magnesium oxide (MgO) as a catalyst. The resultant carbon nano rods were purified and characterized using energy dispersive X-ray spectroscopy (EDX), X-ray powder diffraction (XRD). The surface characteristics of carbon rods were observed with the Field emission scanning electron microscopy (FESEM). The carbon was evenly spread and had the highest concentration from SEM-EDX characterization. The results of XRD and FESEM have shown that carbon Nano rods (CNRs) were present in Nano figures, synthesized at 1000 ° C and with pyrolysis temperature 400° C. One of t

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Publication Date
Fri Feb 08 2019
Journal Name
Iraqi Journal Of Laser
Enhancement of Episiotomy Healing Using (790-805) nm Diode Laser as a Supplementary Treatment
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To show the impact of 790-805 nm diode laser irradiations on wound healing as a supplementary treatment in women underwent episiotomies, and to assess the laser parameters that were used .Material and methods: Eighteen female patients were included in this study; all of them underwent mediolateral episiotomy. Ten patients received laser therapy- diode laser (K Laser) (790-805) nm in CW mode of operation (and eight patients were the control group. Spot size of 8mm, time for exposure for each spot was 30 seconds. The power used was 0.6 W .The power density for each spot of treatment was 1.19 W/cm2 per session (non contact mode of application of laser therapy).The group studied received 2 sessions of laser radiation, day 4, and day 8 after

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Publication Date
Sun Jan 01 2023
Journal Name
International Journal Of Economics And Finance Studies
THE ROLE OF TARGET COST MANAGEMENT APPROACH IN REDUCING COSTS FOR THE ACHIEVEMENT OF COMPETITIVE ADVANTAGE AS A MEDIATOR: AN APPLIED STUDY OF THE IRAQI ELECTRICAL INDUSTRY
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Publication Date
Sun Jan 02 2022
Journal Name
Neuroquantology
Treatment of primary trigeminal neuralgia: A comparative study of microvascular decompression surgery and stereotactic gamma knife radiosurgery
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Objectives To compare the clinical efficacy of microvascular decompression surgery (MVD) and gamma knife radiosurgery (GKR) as a treatment for patients with primary trigeminal neuralgia (TN) and evaluate the outcome regarding pain relief, recurrence, and complications with both modalities of treatment. Patients and Methods A randomized prospective study conducted in SaadAlwitry Neurosciences Hospital, Baghdad, Iraq. Eighty-four patients with TN from January 2016 to January 2018, 45 patients had GKR while 39 patients treated with MVD. The pain evaluated pre-and post-operatively using the Barrow Neurological Institute Pain Intensity scale (BNIPI), visual analog scale (VAS) and Brief Pain Inventory Facial (BPI-Facial) scoring systems. In GKR p

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Publication Date
Thu Oct 01 2009
Journal Name
Jssdds
Topical 10% lactic acid solution in the treatment of pityriasis versicolor in comparison with topical 1% clotrimazol solution (single-blind, comparative and therapeutic study)
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KE Sharquie, AA Noaimi, AM Oweid, JSSDDS, 2009 - Cited by 2

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Publication Date
Fri May 22 2026
Journal Name
Journal Of Physical Education
The Effect of Using Especial Exercises Suggested for Developing of Accuracy Direction by Fencing in Foil for the Players of the National Team of the Young who Handicap
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Publication Date
Wed Mar 29 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Effect of Heterogeneity on Capillary Pressure and Relative Permeability Curves in Carbonate Reservoirs. A Case Study for Mishrif Formation in West Qurna/1 Oilfield, Iraq
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The special core analysis tests were accomplished on a set of core plugs for Mishrif Formation (mA, mB1, and mB2cde/mC units) in West Qurna/1 oilfield, southern Iraq. Oil relative permeability (Kro) data and the Corey-type fit of the data as functions of the brine saturation at the core outlet face for individual samples in the water-oil imbibition process to estimate relative permeability measurements by the centrifuge method were utilized. Identical correlations for oil and water relative permeabilities were extracted by steady-state and unsteady-state methods. For the mA samples, the gas-water capillary pressure curves were within a narrow range (almost identical) indicating that mA is a homogeneous unit. Kro curves for three mB2

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Publication Date
Wed Mar 29 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Effect of Heterogeneity on Capillary Pressure and Relative Permeability Curves in Carbonate Reservoirs. A Case Study for Mishrif Formation in West Qurna/1 Oilfield, Iraq
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The special core analysis tests were accomplished on a set of core plugs for Mishrif Formation (mA, mB1, and mB2cde/mC units) in West Qurna/1 oilfield, southern Iraq. Oil relative permeability (Kro) data and the Corey-type fit of the data as functions of the brine saturation at the core outlet face for individual samples in the water-oil imbibition process to estimate relative permeability measurements by the centrifuge method were utilized. Identical correlations for oil and water relative permeabilities were extracted by steady-state and unsteady-state methods. For the mA samples, the gas-water capillary pressure curves were within a narrow range (almost identical) indicating that mA is a homogeneous unit. Kro curves for thr

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Publication Date
Tue Apr 02 2019
Journal Name
Artificial Intelligence Research
A three-stage learning algorithm for deep multilayer perceptron with effective weight initialisation based on sparse auto-encoder
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A three-stage learning algorithm for deep multilayer perceptron (DMLP) with effective weight initialisation based on sparse auto-encoder is proposed in this paper, which aims to overcome difficulties in training deep neural networks with limited training data in high-dimensional feature space. At the first stage, unsupervised learning is adopted using sparse auto-encoder to obtain the initial weights of the feature extraction layers of the DMLP. At the second stage, error back-propagation is used to train the DMLP by fixing the weights obtained at the first stage for its feature extraction layers. At the third stage, all the weights of the DMLP obtained at the second stage are refined by error back-propagation. Network structures an

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