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

• Genomics & Informatics
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• 제12권2호
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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.

• 한국콘텐츠학회논문지
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• 제8권12호
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• pp.441-448
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• 2008

분자 도킹 실험은 일반적으로 계산 량이 매우 많아 슈퍼 컴퓨팅 파워를 요구하는 실험이다. 따라서 시간이 많이 소요되기 때문에 일반적으로 CPU가 탑재된 컴퓨터를 여러 대 묶어서 사용하는 분산 환경 혹은 그리드 환경에서 실험을 수행하고 있다. 이와 같은 실험 환경은 시간적, 공간적 제약성이 많아 일반적으로 과학자들이 접근하기가 어렵다. 그래서 근래에는 많은 CPU를 사용하기 보다는 월등히 성능이 높은 GPU를 병렬 화하여 과학 분야에 계산하는 연구가 매우 활발히 이루어지고 있는 추세이다. CUDA는 병렬 GPU 프로그래밍을 가능하게 하는 공개 기술이다. 본 논문에서는 이러한 CUDA 기술을 사용하여 분자 도킹 실험을 할 수 있는 시스템을 제안한다. 또한, 분자 도킹 실험에 있어서 중요한 에너지 최소화 계산을 병렬 화하는 알고리즘을 제안한다. 이와 같은 실험을 검증하기 위해 본 논문에서는 일반적인 CPU에서 분자 도킹 실험 시간과 본 논문에서 제안한 병렬 CPU 기반의 분자 도킹 시간을 비교 분석 하였다.

• Bulletin of the Korean Chemical Society
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• 제34권3호
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• pp.899-906
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• 2013

Using generated conformations from docking analysis by Gold algorithm, some 3D-QSAR models; CoMFA and CoMSIA have been created on 39 N-benzoylated phenoxazines and phenothiazines, including their S-oxidized analogues. These molecules inhibit the polymerization of tubulin into microtubules and thus they have been studied for the development of antitumor drugs. Training set for the CoMFA and CoMSIA models using 30 docked conformations gives $q^2$ Leave one out (LOO) values of 0.756 and 0.617, and $r^2$ ncv values of 0.988 and 0.956, respectively. The ability of prediction and robustness of the models were evaluated by test set, cross validation (leave-one-out and leave-ten-out), bootstrapping, and progressive scrambling approaches. The all-orientation search (AOS) was used to achieve the best orientation to minimize the effect of initial orientation of the structures. The docking results confirmed CoMFA and CoMSIA contour maps. The docking and 3D-QSAR studies were thoroughly interpreted and discussed and confirmed the experimental $pIC_{50}$ values.

• 대한조선학회 특별논문집
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• 대한조선학회 2006년도 특별논문집
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• pp.89-96
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• 2006

The objective of this paper is to find out a reasonable method for docking analysis of ships. The characteristics of reaction force distribution under docking condition are investigated by carrying out parametric study. To assess the allowable reaction force on keel block from structural strength point of view, two kinds of structural assessment methods are proposed in accordance with expected collapse pattern. In order to verify the proposed method, linear buckling and elasto-plastic large deflection analyses of typical double bottom structure are carried out and the results are compared.

• 대한화학회지
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• 제62권2호
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• pp.106-112
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• 2018

Ice-binding proteins have an affinity for ice. They create a gap between the melting and freezing points by inhibiting the growth of ice, known as thermal hysteresis (TH). Interestingly, moderately active LeIBP and hyperactive FfIBP are almost identical in primary and tertiary structures, but differ in TH activity. The TH of FfIBP is tenfold higher than that of LeIBP, due to a subtle difference in their ice-binding motifs. To further evaluate the difference in TH, the interactions were investigated by ice-etching and molecular docking. Ice-etching showed that FfIBP binds to the primary and secondary prism, pyramidal, and basal planes; previously, LeIBP was found to bind to the basal and primary prism planes. Docking analysis using shape complementarity (Sc) showed that the hyperactive FfIBP had higher Sc values for all four ice planes than LeIBP, which is comparable with TH. Docking can be used to describe the hyperactivity of IBPs.

• 한국항해항만학회지
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• 제48권2호
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• pp.116-124
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• 2024

Automatic docking of small planing ship is a critical aspect of maritime operations, requiring accurate prediction of motion states to ensure safe and efficient maneuvers. This study investigates the use of Artificial Neural Network (ANN) to predict motion state of a small planing ship to enhance navigation automation in port environments. To achieve this, simulation tests were conducted to control a small planing ship while docking at various heading angles in calm water and in waves. Comprehensive analysis of the ANN-based predictive model was conducted by training and validation using data from various docking situations to improve its ability to accurately capture motion characteristics of a small planing ship. The trained ANN model was used to predict the motion state of the small planning ship based on any initial motion state. Results showed that the small planing ship could dock smoothly in both calm water and waves conditions, confirming the accuracy and reliability of the proposed method for prediction. Moreover, the ANN-based prediction model can adjust the dynamic model of the small planing ship to adapt in real-time and enhance the robustness of an automatic positioning system. This study contributes to the ongoing development of automated navigation systems and facilitates safer and more efficient maritime transport operations.

• Bulletin of the Korean Chemical Society
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• 제29권8호
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• pp.1499-1504
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• 2008

Pyrazine derivatives bind to b-RAF receptor which is important in cancer therapy. The ligand-receptor interactions have been studied by comparative molecular field analysis (CoMFA) and molecular docking methods. Applying conventional ligand-based alignment schemes for the whole set was not successful. However, QM and DFT results suggested that some ligands have electrostatic interaction while others have steric interactions. On the basis of these results, we divided the dataset into two subsets. Electrostatic effect was found to be important in one set while steric effect for the other. Best docking modes were obtained for each subset based on the available crystal structure. These receptor-guided CoMFA models propose an interesting possibility which is difficult to obtain otherwise. i.e., in one binding mode the electrostatic interaction plays a key role for one subset ($q^2$ = 0.46, $r^2$ = 0.98), while in another binding mode steric effect is important with another subset ($q^2$ = 0.43, $r^2$ = 0.74).

• 통합자연과학논문집
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• 제11권2호
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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.

• Genomics & Informatics
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• 제13권2호
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• pp.60-67
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• 2015

The leading cause of cancer mortality globally amongst the women is due to human papillomavirus (HPV) infection. There is need to explore anti-cancerous drugs against this life-threatening infection. Traditionally, different natural compounds such as withaferin A, artemisinin, ursolic acid, ferulic acid, (-)-epigallocatechin-3-gallate, berberin, resveratrol, jaceosidin, curcumin, gingerol, indol-3-carbinol, and silymarin have been used as hopeful source of cancer treatment. These natural inhibitors have been shown to block HPV infection by different researchers. In the present study, we explored these natural compounds against E6 oncoprotein of high risk HPV18, which is known to inactivate tumor suppressor p53 protein. E6, a high throughput protein model of HPV18, was predicted to anticipate the interaction mechanism of E6 oncoprotein with these natural inhibitors using structure-based drug designing approach. Docking analysis showed the interaction of these natural inhibitors with p53 binding site of E6 protein residues 108-117 (CQKPLNPAEK) and help reinstatement of normal p53 functioning. Further, docking analysis besides helping in silico validations of natural compounds also helped elucidating the molecular mechanism of inhibition of HPV oncoproteins.