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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
Thu Jan 01 2015
Journal Name
Energy Sources, Part A: Recovery, Utilization, And Environmental Effects
Ultra Deep Hydrotreatment of Iraqi Vacuum Gas Oil Using a Modified Catalyst
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A set of hydro treating experiments are carried out on vacuum gas oil in a trickle bed reactor to study the hydrodesulfurization and hydrodenitrogenation based on two model compounds, carbazole (non-basic nitrogen compound) and acridine (basic nitrogen compound), which are added at 0–200 ppm to the tested oil, and dibenzotiophene is used as a sulfur model compound at 3,000 ppm over commercial CoMo/ Al2O3 and prepared PtMo/Al2O3. The impregnation method is used to prepare (0.5% Pt) PtMo/Al2O3. The basic sites are found to be very small, and the two catalysts exhibit good metal support interaction. In the absence of nitrogen compounds over the tested catalysts in the trickle bed reactor at temperatures of 523 to 573 K, liquid hourly space v

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Publication Date
Wed Dec 31 2014
Journal Name
Al-khwarizmi Engineering Journal
Energy Saving of Heat Gain by Using Buried Pipe Inside a Roof
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Abstract

    This work deals with a numerical investigation to evaluate the utilization of a water pipe buried inside a roof to reduce the heat gain and minimize the transmission of heat energy inside the conditioning space in summer season.     The numerical results of this paper showed that the reduction in heat gain and energy saving could be occurred with specific values of parameters, like the number of pipes per square meter, the ratio of pipe diameter to the roof thickness, and the pipe inlet water temperature. Comparing with a normal roof (without pipes), the results indicated a significant reduction in energy heat gain which is about 37.8% when the number of pipes per m

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Publication Date
Tue Mar 04 2014
Journal Name
International Journal Of Advanced Computing
User Authentication Approach using a Combination of Unigraph and Digraph Keystroke Features
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In Computer-based applications, there is a need for simple, low-cost devices for user authentication. Biometric authentication methods namely keystroke dynamics are being increasingly used to strengthen the commonly knowledge based method (example a password) effectively and cheaply for many types of applications. Due to the semi-independent nature of the typing behavior it is difficult to masquerade, making it useful as a biometric. In this paper, C4.5 approach is used to classify user as authenticated user or impostor by combining unigraph features (namely Dwell time (DT) and flight time (FT)) and digraph features (namely Up-Up Time (UUT) and Down-Down Time (DDT)). The results show that DT enhances the performance of digraph features by i

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Publication Date
Wed May 10 2023
Journal Name
Journal Of Engineering
Vibration Control Analysis of a Smart Flexible Cantilever Beam Using Smart Material
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This paper features the modeling and design of a pole placement and output Feedback control technique for the Active Vibration Control (AVC) of a smart flexible cantilever beam for a Single Input Single Output (SISO) case. Measurements and actuation actions done by using patches of piezoelectric layer, it is bonded to the master structure as sensor/actuator at a certain position of the cantilever beam.
The smart structure is modeled based on the concept of piezoelectric theory, Bernoulli -Euler beam theory, using Finite Element Method (FEM) and the state space techniques. The number of modes is reduced using the controllability and observability grammians retaining the first three
dominant vibratory modes, and for the reduced syste

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Publication Date
Tue Dec 01 2015
Journal Name
Solar Energy
A review of studies on using nanofluids in flat-plate solar collectors
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Continuous escalation of the cost of generating energy is preceded by the fact of scary depletion of the energy reserve of the fossil fuels and pollution of the environment as developed and developing countries burn these fuels. To meet the challenge of the impending energy crisis, renewable energy has been growing rapidly in the last decade. Among the renewable energy sources, solar energy is the most extensively available energy, has the least effect on the environment, and is very efficient in terms of energy conversion. Thus, solar energy has become one of the preferred sources of renewable energy. Flat-plate solar collectors are one of the extensively-used and well-known types of solar collectors. However, the effectiveness of the coll

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Publication Date
Mon Jul 01 2013
Journal Name
2013 35th Annual International Conference Of The Ieee Engineering In Medicine And Biology Society (embc)
Protocol for site selection and movement assessment for the myoelectric control of a multi-functional upper-limb prosthesis
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Publication Date
Thu Aug 05 2021
Journal Name
International Journal Of Renewable Energy Development
Desalination of Agricultural Wastewater by Solar Adsorption System: A Numerical Study
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There are still areas around the world suffer from severe shortage of freshwater supplies. Desalination technologies are not widely used due to their high energy usage, cost, and environmental damaging effects. In this study, a mathematical model of single-bed adsorption desalination system using silica gel-water as working pair is developed and validated via earlier experiments. A very good match between the model predictions and the experimental results is recorded. The objective is to reveal the factors affecting the productivity of fresh water and cooling effect in the solar adsorption system. The proposed model is setup for solving within the commercially-available software (Engineering Equation Solver). It is implemented to so

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Publication Date
Thu Sep 15 2022
Journal Name
Bionatura
Chronic Myeloid Leukemia: A retrospective study of clinical and pathological features
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Chronic myeloid leukemia (CML), is one of the myeloproliferative disorders with a characteristic cytogenetic abnormality resulting in the BCR-ABL fusion gene. Imatinib Mesylate is an effective agent for treating patients in all stages of CML. According to the annual Iraqi cancer registry 2019, the total number of chronic myeloproliferative disorders was 338. The percentage and incidence rates were 0.94% and 0.86%, respectively, with a higher incidence rate in males than females (1.12 in males and 0.60 in females). In this registry, no details about CML, so this study aimed to estimate the number of CML patients who attended the national center of hematology from 2005 until 2020 and investigate their epidemiological and clinic-pathol

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Publication Date
Mon Nov 01 2021
Journal Name
Journal Of Language And Linguistic Studies
A Pragma-Linguistic Study of Suggestive Ambiguity in Selected Political Texts.
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Suggestive ambiguity is a strategy of defense and maneuvering as it provides the speaker both protection and function. To put it differently, it helps the speaker to say whatever he likes and at the same time gives his opponents and friends the interpretation they desire. This is possible due to the flexibility of the linguistic expressions that the speaker uses. To be more clear, the context of situation, peoples' background and world knowledge interact with the significance of the linguistic expressions reaching an allusive situation where two interpretations, positive and negative, are available to the addressees. Such situation enables the addressers to implicate different ideas or messages, accusations, inciting violence, etc. The pres

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Publication Date
Wed Jun 30 2010
Journal Name
Al-kindy College Medical Journal
A prospective study of colonoscopic examination at al-kindy teaching hospital
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Background: Fiber-optic endoscopy is an important
investigation of the large intestine, whether or not the
radiologist (barium enema) has discovered a lesion in
the bowel. Colonoscopy affords a unique opportunity
to direct visualization of entire colonic mucosa. At
the same time, the physician can obtain biopsy specimens, remove polyps, and decompress volvuli.
Most experienced endoscopists and well prepared
patients can reach the cecum in over 90% of patients.
If colonoscopy is properly performed, it has a low
risk of complications, such as perforation and bleeding.
Methods: A total of 70 consecutive patients admitted
to Endoscopy department at Al-Kindy Teaching hospital from September- 2008 to July-2009.

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