• International Journal of Aeronautical and Space Sciences
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• v.12 no.1
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• pp.43-56
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• 2011

An integrated system composed of guidance, navigation and control (GNC) system for autonomous proximity operations and the docking of two spacecraft was developed. The position maneuvers were determined through the integration of the state-dependent Riccati equation formulated from nonlinear relative motion dynamics and relative navigation using rendezvous laser vision (Lidar) and a vision sensor system. In the vision sensor system, a switch between sensors was made along the approach phase in order to provide continuously effective navigation. As an extension of the rendezvous laser vision system, an automated terminal guidance scheme based on the Clohessy-Wiltshire state transition matrix was used to formulate a "V-bar hopping approach" reference trajectory. A proximity operations strategy was then adapted from the approach strategy used with the automated transfer vehicle. The attitude maneuvers, determined from a linear quadratic Gaussian-type control including quaternion based attitude estimation using star trackers or a vision sensor system, provided precise attitude control and robustness under uncertainties in the moments of inertia and external disturbances. These functions were then integrated into an autonomous GNC system that can perform proximity operations and meet all conditions for successful docking. A six-degree of freedom simulation was used to demonstrate the effectiveness of the integrated system.

• Journal of Integrative Natural Science
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• v.8 no.3
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• pp.209-213
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• 2015

Influenza A virus (H1N1) causes and spreads infectious diseases and becomes a major health threat in humans. Among the subtypes of influenza virus, neuraminidase (NA) plays an important role in viral life cycle and becomes an attractive therapeutic target. Currently two NA inhibitors namely Zanamivir and Oseltamivir are available for treating infectious diseases. Recently five naturally derived polyphenols extracted from Phellinus baumii was reported as inhibitors against NA. Molecular docking is powerful tool in computer aided drug designing which aids in exploring and elucidating the properties of the molecules from their 3D structure. Hence, in the present study, molecular docking was carried out on reported polyphenols isolated from ethanolic extract of fruiting bodies of Phellinus baumii. The objective of this work was to study the interaction and to propose the binding mode of these compounds within the binding site of H1N1 neuraminidase. The results showed these compounds had better binding energy and H-bond interactions with the important active site residues of the receptor which authenticate these compounds contributes to inhibitory activity of neuraminidase to treat influenza infection.

• Journal of the Korean Society for Aeronautical & Space Sciences
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• v.36 no.11
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• pp.1072-1078
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• 2008

An adaptive control algorithm for spacecraft rendezvous and docking in a Keplerian orbit is presented. The equations of relative motion of two spacecrafts expressed in a local-vertical-local-horizontal rectangular frame are converted to a general Hamiltonian form, then an adaptive control method developed for the uncertain Hamiltonian system is applied to the rendezvous and docking problem. A smooth projection algorithm is applied to keep the parameter estimates inside a singularity-free region, and a numerical example shows that the developed controller successfully deals with the unknown mass of the chaser spacecraft.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.210-218
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• 2004

Poly(ADP-ribose)polymerase-1 (PARP-1) is a nuclear enzyme involved in various physical functions related to genomic repair, and PARP inhibitors have therapeutic application in a variety of neurological diseases. Docking and the QSAR (quantitative structure-activity relationships) studies for 52 PARP-1 inhibitors were conducted using FlexX algorithm, comparative molecular field analysis (CoMFA), and hologram quantitative structure-activity relationship analysis (HQSAR). The resultant FlexX model showed a reasonable correlation (r$^{2}$ = 0.701) between predicted activity and observed activity. Partial least squares analysis produced statistically significant models with q$^{2}$ values of 0.795 (SDEP=0.690, r$^{2}$=0.940, s=0.367) and 0.796 (SDEP=0.678, r$^{2}$ = 0.919, s=0.427) for CoMFA and HQSAR, respectively. The models for the entire inhibitor set were validated by prediction test and scrambling in both QSAR methods. In this work, combination of docking, CoMFA with 3D descriptors and HQSAR based on molecular fragments provided an improved understanding in the interaction between the inhibitors and the PARP. This can be utilized for virtual screening to design novel PARP-1 inhibitors.

• Journal of Integrative Natural Science
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• v.11 no.2
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• pp.121-129
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• 2018

CXCR6 is a major target in drug design as it is a determinant receptor in many diseases like AIDS, Type I Diabetes, some cancer types, atherosclerosis, tumor formation, liver disease and steatohepatitis. In this study, we propose the active site residues of CXCR6 molecule. We employed homology modelling and molecular docking approach to generate the 3D structure for CXCR6 and to explore its interaction between the antagonists and agonists. 3D models were generated using 14 different templates having high sequence identity with CXCR6. Surflex docking studies using pyridine and pyrimidine derivatives enabled the analysis of the binding site and finding of the important residues involved in binding. 3D structure of CXCL16, a natural ligand for CXCR6, was modelled using PHYRE and protein - protein docking was performed using ClusPro. The residues which were found to be crucial in interaction with the ligand are THR110, PHE113, TYR114, GLN160, GLN195, CYS251 and SER255. This study can be used as a guide for therapeutic studies of human CXCR6.

• Asian-Australasian Journal of Animal Sciences
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• v.6 no.1
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• pp.79-86
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• 1993

Twelve docked and 12 intact Najdi lambs of equal numbers of males and females were slaughtered at 40 kg shorn shrunk body weight, Lipid in all empty body fat components; namely, subcutaneous, intermuscular, intramuscular, omental, mesenteric, channel, perirenal, pericardial, tail, viscera, bone and hide, were determined. Except for ram lambs, which had a lower percentage of lipid in intermuscular partition in loin cut, sex did not influence the relative proportion of subcutaneous or intermuscular fat in each wholesale cut. The data also showed that docking did not change the distribution of lipid in intermuscular and intramuscular fat partitions in each wholesale cut. Docked lambs tended to accumulate lower proportions of the lipid in subcutaneous fat component in the cuts located along the dorsal line than intact lambs. The total amount of lipid deposited in the empty body of ewe lamb was heavier in weight than that of ram lamb. Docking had no effect on the distribution of total lipid in the empty body, except for subcutaneous fat component, being greater in docked lambs than did intact ones. Generally, the highest proportion of fat was associated with subcutaneous depot followed, in order, by intermuscular, mesenteric, tail, intramuscular and omental fat partitions.

• Journal of Microbiology and Biotechnology
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• v.25 no.1
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• pp.44-49
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• 2015

Thermostable enzymes derived from Thermotoga maritima have attracted worldwide interest for their potential industrial applications. Structural analysis and docking studies were preformed on T. maritima β-glucosidase enzyme with cellobiose and pNP-linked substrates. The 3D structure of the thermostable β-glucosidase was downloaded from the Protein Data Bank database. Substrates were downloaded from the PubCehm database and were minimized using MOE software. Docking of BglA and substrates was carried out using MOE software. After analyzing docked enzyme/substrate complexes, it was found that Glu residues were mainly involved in the reaction, and other important residues such as Asn, Ser, Tyr, Trp, and His were involved in hydrogen bonding with pNP-linked substrates. By determining the substrate recognition pattern, a more suitable β-glucosidase enzyme could be developed, enhancing its industrial potential.

• Journal of Integrative Natural Science
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• v.3 no.1
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• pp.49-53
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• 2010

Molecular docking is a critical event which mostly forms Van der waals complex in molecular recognition. Since the majority of developed drugs are small molecules, docking them into proteins has been a prime concern in drug discovery community. Since the binding pose space is too vast to cover completely, many search algorithms such as genetic algorithm, Monte Carlo, simulated annealing, distance geometry have been developed. Proper evaluation of the quality of binding is an essential problem. Scoring functions derived from force fields handle the ligand binding prediction with the use of potential energies and sometimes in combination with solvation and entropy contributions. Knowledge-based scoring functions are based on atom pair potentials derived from structural databases. Forces and potentials are collected from known protein-ligand complexes to get a score for their binding affinities (e.g. PME). Empirical scoring functions are derived from training sets of protein-ligand complexes with determined affinity data. Because non of any single scoring function performs generally better than others, some other approaches have been tried. Although numerous scoring functions have been developed to locate the correct binding poses, it still remains a major hurdle to derive an accurate scoring function for general targets. Recently, consensus scoring functions and target specific scoring functions have been studied to overcome the current limitations.

• Genomics & Informatics
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• v.12 no.4
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• pp.276-282
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• 2014

The disease tuberculosis, caused by Mycobacterium tuberculosis (MTB), remains a major cause of morbidity and mortality in developing countries. The evolution of drug-resistant tuberculosis causes a foremost threat to global health. Most drug-resistant MTB clinical strains are showing resistance to isoniazid and rifampicin (RIF), the frontline anti-tuberculosis drugs. Mutation in rpoB, the beta subunit of DNA-directed RNA polymerase of MTB, is reported to be a major cause of RIF resistance. Amongst mutations in the well-defined 81-base-pair central region of the rpoB gene, mutation at codon 450 (S450L) and 445 (H445Y) is mainly associated with RIF resistance. In this study, we modeled two resistant mutants of rpoB (S450L and H445Y) using Modeller9v10 and performed a docking analysis with RIF using AutoDock4.2 and compared the docking results of these mutants with the wild-type rpoB. The docking results revealed that RIF more effectively inhibited the wild-type rpoB with low binding energy than rpoB mutants. The rpoB mutants interacted with RIF with positive binding energy, revealing the incapableness of RIF inhibition and thus showing resistance. Subsequently, this was verified by molecular dynamics simulations. This in silico evidence may help us understand RIF resistance in rpoB mutant strains.

• Genomics & Informatics
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• v.12 no.2
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• pp.64-70
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• 2014

Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. The life-threatening infection caused by HPV demands the need for designing anticancerous drugs. In the recent years, different compounds from natural origins, such as carrageenan, curcumin, epigallocatechin gallate, indole-3-carbinol, jaceosidin, and withaferin, have been used as a hopeful source of anticancer therapy. These compounds have been shown to suppress HPV infection by different researchers. In the present study, we explored these natural inhibitors against E6 oncoprotein of high-risk HPV-16, which is known to inactivate the p53 tumor suppressor protein. A robust homology model of HPV-16 E6 was built to anticipate the interaction mechanism of E6 oncoprotein with natural inhibitory molecules using a structure-based drug designing approach. Docking analysis showed the interaction of these natural compounds with the p53-binding site of E6 protein residues 113-122 (CQKPLCPEEK) and helped the restoration of p53 functioning. Docking analysis, besides helping in silico validation of natural compounds, also helps understand molecular mechanisms of protein-ligand interactions.