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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 May 05 2016
Journal Name
International Journal Of Science And Research (ijsr)
Synthesis, Characterization and Antimicrobial Activity Studies of Mixed-1,10-phenanthroline-Mn(II),Co(II), Cu(II), Ni(II) and Hg(II) Complexes with Schiff Base[2,2'-(1Z,1'Z)-(biphenyl-4,4'-diylbis(azan-1-yl-1-ylidene))bis(methan-1-yl-1-ylidene)diphenol]
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Publication Date
Sat May 07 2016
Journal Name
International Journal Of Science And Research
Synthesis, Characterization and Antimicrobial Activity Studies of Mixed-1,10-phenanthroline- Mn(II),Co(II), Cu(II), Ni(II) and Hg(II) Complexes with Schiff Base[2,2'-(1Z,1'Z)-(biphenyl-4,4'- diylbis(azan-1-yl-1-ylidene))bis(methan-1-yl-1- ylidene)diphenol]
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Abstract: The M(II) complexes [M2(phen)2(L)(H2O)2Cl2] in (2:1:2 (M:L:phen) molar ratio, (where M(II) =Mn(II), Co(II), Cu(II), Ni(II) and Hg(II), phen = 1,10-phenanthroline; L = 2,2'-(1Z,1'Z)-(biphenyl-4,4'-diylbis(azan-1-yl-1-ylidene))bis(methan-1-yl-1- ylidene)diphenol] were synthesized. The mixed complexes have been prepared and characterized using 1H and13C NMR, UV/Visible, FTIR spectra methods and elemental microanalysis, as well as magnetic susceptibility and conductivity measurements. The metal complexes were tested in vitro against three types of pathogenic bacteria microorganisms: Staphylococcus aurous, Escherichia coli, Bacillussubtilis and Pseudomonasaeroginosa to assess their antimicrobial properties. From this study shows that a

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Publication Date
Sun Feb 22 2026
Journal Name
Sciences Journal Of Physical Education
The impact of a proposal for the curriculum dictated by some of the barriers to the development of motor skills
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The impact of a proposal for the curriculum dictated by some of the barriers to the development of motor skillsA. M. D. Huda Ibrahim RezoukiM. M. Susan Salim DawoodIs the childhood of the most important and most fertile stage of basic education because of their significant impact in building a base on which the stated origin of sound in the early stages older age because the baby at this stage be very vulnerability to environmental factors different surroundings in which to leave their mark on his life in the stages of life other.The Gymnastics of sports long-term training, which begins between the ages very early relative to the rest of other games to reach the stage of the tournament from the age of 13-17 years almost to the women, this a

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Publication Date
Mon May 01 2023
Journal Name
Chemical Engineering Research And Design
Treatment of petroleum refinery wastewater by electrofenton process using a low cost porous graphite air-diffusion cathode with a novel design
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Publication Date
Sat Sep 01 2018
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The role of risk management programs in Dealing With risks at international airports: An Applied research at Baghdad International Airport
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The objective of the research is to identify the efficiency of risk management in various names at Baghdad International Airport in the face of various risks (financial - technical - human - natural ..) facing the sample of the search of the General Establishment of Civil Aviation and the Iraqi Airways Company where the researcher identified the hypothesis that summarizes There is a significant significant correlation between risk management, risk management and risk review and assessment. The researcher used the means of research from observation and interviews with the relevant officials in this field, as well as used the questionnaire and distributed a sample of 170 employees in the field of risk management (SMS Department) in Iraqi A

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Publication Date
Fri Sep 09 2022
Journal Name
Surgical Neurology International
WhatsApp as a remote patient-monitoring tool in low- and middle-income countries: Experience from the cerebrovascular surgery service in Iraq
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Publication Date
Thu Jun 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Customers emotional blackmail and reduce it the new product- study of the opinions of a sample of customers who deal with peak economy for household items in najaf al Ashraf
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The challenges facing today's multi-customer and this is due to the multiplicity of products and speed in launching new products so search came to reveal the  reveal the of the new product classification standards through a relationship (good products, low interest products, useful products and products desired) and the customer emotionally blackmail through deportation (fear, obligation and guilt). dentified the problem of the research in several questions focused on the nature of the relationship between the variables of research, and for that outline supposedly to search it expresses the head of one hypothesis and branched out of which four hypotheses subset, but in order to ensure the validity of the ass

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Publication Date
Sun Jun 05 2016
Journal Name
Baghdad Science Journal
Synthesis, Spectral Study and Theoretical Treatment of Some Mixing Ligand Complexes of Quinaldic Acid and 1, 10-Phenathroline
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Metal complexes of Cu (II), Fe (III) and Mn (II) with Quinaldic acid (L1) and 1, 10-Phenathroline (L2) are synthesized and characterized by standaral physic- chemical procedures (element analysis, metal analysis, FTIR, Uv-Vis, magnetic moment and conductometeric measurements). On the base of these studies, mononuclear and six coordinated octahedral geometry and nonelectrolyte of these complexes have been proposed. The standard heat of formation (?Hºf) and binding energy (?Eb) for the free ligands and their complexes are calculated by using the PM3 method at 273K of Hyperchem.-8 program. The complexes are more stable than their ligands. Moreover, the electrostatic potential of free ligands are measured to investigate the reactive site of th

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Publication Date
Sat Dec 01 2018
Journal Name
Political Sciences Journal
A study in Tunisian - Iraqi Relations and its role in determining strategies for dealing with conflict and peace situations
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If the State attaches great importance to its foreign relations and intends to strengthen them in order to ensure the achievement of the highest national goals and interests. External relations between countries are one of the most prominent features of foreign policy, which depends on a combination of internal and external factors, the modern relations between Tunisia and Tunisia, which goes back to the pre-independence of Tunisia, when Iraq was a supporter of Tunisia's independence from France in the 1940s, Although these relations did not cause any disturbance by the two countries, but they remained weak relations did not develop in all areas except the sports and cultural field, which we will determine the reasons and the pos

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Publication Date
Sun Dec 31 2023
Journal Name
Iraqi Geological Journal
Advanced Geostatistical Techniques for Building 3D Geological Modeling: A Case Study from Cretaceous Reservoir in Bai Hassan Oil Field
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A 3D Geological model was generated using an advanced geostatistical method for the Cretaceous reservoir in the Bai Hassan oil field. In this study, a 3D geological model was built based on data from four wells for the petrophysical property distribution of permeability, porosity, water saturation, and NTG by using Petrel 2021 software. The geological model was divided into a structural model and a property model. The geological structures of the cretaceous reservoir in the Bai Hassan oil field represent elongated anticline folds with two faults, which had been clarified in the 3D Structural model. Thirteen formations represent the Cretaceous reservoir which includes (Shiranish, Mashurah, U.kometan, Kometan Shale, L. Kometan, Gulnen

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