• 센서학회지
• /
• 제26권3호
• /
• pp.199-203
• /
• 2017

In this paper, we developed an underwater localization system for underwater robot docking using the electromagnetic wave attenuation model. Electromagnetic waves are generally known to be impossible to use in water environment. However, according to the conclusions of the previous studies on the attenuation characteristics in underwater, the attenuation pattern is uniform and its model was accurately proposed and verified in 3-dimensional space via the omnidirectional antenna. In this paper, a docking structure and localization sensor system are developed for a widely used cone type docking mechanism. First, we fabricated electromagnetic wave range sensor transmit modules. And a mobile sensor node is equipped with unmanned underwater vehicle(UUV)s. The mobile node senses the four different signal strength (RSS: Received Signal Strength) from fixed nodes, and the obtained RSS data are transformed to each distance information using the 3-Dimensional EM wave attenuation model. Then, the relative localization between the docking area and underwater robot can be achieved according to optimization algorithm. Finally, experimental results show the feasibility of the proposed localization system for the docking induction by comparing the errors in the actual position of the mobile node and the theoretical position through the model.

• 한국생물물리학회:학술대회논문집
• /
• 한국생물물리학회 1996년도 정기총회 및 학술발표회
• /
• pp.32-32
• /
• 1996

Molecular docking studies were performed for a humanized HBV Pre-S2 antibody and its antigen adr. Antigen structure was taken from NMR experiment and antibody structure was determined by using homology technique. At first step, Grid search was performed for finding energetically favorable orientations antigen. (omitted)

• 한국생물정보학회:학술대회논문집
• /
• 한국생물정보시스템생물학회 2004년도 The 3rd Annual Conference for The Korean Society for Bioinformatics Association of Asian Societies for Bioinformatics 2004 Symposium
• /
• pp.210-218
• /
• 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.

• 통합자연과학논문집
• /
• 제11권2호
• /
• pp.121-129
• /
• 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.

• 대한화학회지
• /
• 제65권2호
• /
• pp.106-112
• /
• 2021

12 kinds of (-)-catechin derivatives were designed and synthesized. The catechin derivatives were evaluated their antioxidant activities using DPPH method. Most of them showed good antioxidant activity, particularly compounds 1d, 1e and 1j exhibited more activity than butylated hydroxytoluene (BHT). Molecular docking studies for compounds 1d, 1e and 1j with STAT1 showed not only sufficent characteristics binding cavity but also agreement with the observed biological activity. Acording to docking results, the compounds showed greater than hydrogen bonding, hydrophobic interactions, electrostatic interactions, and Van der Waals interactions as compared to the reference compound. They formed hydrogen bonds with important residues such as Lys566, His568, Leu570, and Phe644. The compounds showed a novel hydrogen bonding interaction with Arg649, which was not reported previously. Our results might suggest the compounds could serve as a novel anti-oxidant agent.

• 통합자연과학논문집
• /
• 제8권3호
• /
• pp.204-208
• /
• 2015

Pyrazole, ${\beta}$-lactam, salicidine, pyren and oxazole derivatives exhibit a broad spectrum of biological activities such as antimicrobial, anti-inflammatory and antitumor activities. With growing application on their synthesis and bioactivity, chemists and biologists in recent years have considerable attention on the research of these derivatives. In the view of potential importance of these derivatives, we have crystallized few of the derivatives and its report has been published. The present study focuses on docking studies of these derivatives against COX-2 enzyme. Docking studies using Schrodinger's GLIDE reveals that these derivatives shows better binding energy and score in the defined active site. These results may provide a guiding role to design a lead molecule which may reduce inflamation.

• Bulletin of the Korean Chemical Society
• /
• 제32권7호
• /
• pp.2433-2442
• /
• 2011

The three dimensional quantitative structure activity relationship (3D QSAR) models were developed using Comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and docking studies. The fit of Quinazolinone antifolates inside the active site of modeled bovine dihydrofolate reductase (DHFR) was assessed. Both ligand based (LB) and receptor based (RB) QSAR models were generated, these models showed good internal and external statistical reliability that is evident from the $q^2_{loo}$, $r^2_{ncv}$ and $r^2_{pred}$. The identified key features enabled us to design new Quinazolinone analogues as DHFR inhibitors. This study is a building bridge between docking studies of homology modeled bovine DHFR protein as well as ligand and target based 3D QSAR techniques of CoMFA and CoMSIA approaches.

• Asian Pacific Journal of Cancer Prevention
• /
• 제16권12호
• /
• pp.5005-5006
• /
• 2015

Gastric cancer as one of the most common cancers worldwide has various genetic and environmental risk factors including Helicobacter pylori (H.pylori) infection. Recently, loss of a tumor suppressor gene named promyelocytic leukemia (PML) has been identified in gastric cancer. However, no mutation has been found in this gene in gastric cancer samples. Cag A H.pylori protein has been shown to exert post transcriptional regulation of some tumor suppressor genes. In order to assess such a mechanism for PML degradation, we performed in silico analyses to establish any interaction between PML and Cag A proteins. In silico interaction and docking studies showed that these two proteins may have stable interactions. In addition, we showed that imatinib kinase inhibitor can restore PML function by inhibition of casein kinase 2.

• Bulletin of the Korean Chemical Society
• /
• 제27권2호
• /
• pp.266-272
• /
• 2006

Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were developed for 67 molecules of 2-amino-benzothiazole-6-anilide derivatives against lymphocyte-specific protein tyrosine kinase (P56 LCK). The molecular field analysis (MFA) and receptor surface analysis (RSA) were employed for QSAR studies and the predictive ability of the model was validated by 15 test set molecules. Structure-based investigations using molecular docking simulation were performed with the crystal structure of P56 LCK. Good correlation between predicted fitness scores versus observed activities was demonstrated. The results suggested that the nature of substitutions at the 2-amino and 6-anilide positions were crucial in enhancing the activity, thereby providing new guidelines for the design of novel P56 LCK inhibitors.

• 통합자연과학논문집
• /
• 제15권4호
• /
• pp.179-186
• /
• 2022

The c-Jun N-terminal kinase (JNK3) play major role in neurodegenerative diseases like Alzheimer's disease, Parkinson's disease, cerebral ischemia and other Central Nervous System disorders. Since JNK3 is primarily stated in the brain and stimulated by stress-stimuli, this situation is conceivable that inhibiting JNK3 could be a possible treatment for the mechanisms underlying neurodegenerative diseases. In this study drugs from Zinc15 database were screened to identify the JNK3 inhibitors by Molecular docking and Density functional theory approach. Molecular docking was done by Autodock vina and the ligands were selected based on the binding affinity. Our results identified top ten novel ligands as potential inhibitors against JNK3. Molecular docking revealed that Venetoclax, Fosaprepitant and Avapritinib exhibited better binding affinity and interacting with proposed binding site residues of JNK3. Density functional theory was used to compute the values for energy gap, lowest unoccupied molecular orbital (LUMO), and highest occupied molecular orbital (HOMO). The results of Density functional theory study showed that Venetoclax, Fosaprepitant and Avapritinib serves as a lead compound for the development of JNK3 small molecule inhibitors.