• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2004년도 봄 학술발표논문집 Vol.31 No.1 (A)
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• pp.466-468
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• 2004

Molecular modelling은 시뮬레이션을 통해 온도, 압력 등과 같은 분자 운동에 영향을 미칠 수 있는 요소를 설정한 후 분자의 움직임을 관찰하는 방법으로 신약, 신소재, 고분자 개발에 있어서 연구 개발 기간을 단축하는 효과적인 방법이다. 기존의 molecular modelling 어플리케이션들은 슈퍼컴퓨터나 단일 클러스터를 이용하여 작업을 수행하도록 설계되어 비용과 성능 측면에서 문제점을 가지고 있다. 1590년대 중반 지리적으로 분산되어 있는 광범위한 자원들을 공유하여 장기간 소요되는 컴퓨팅 작업의 성능 향상 및 비용절감을 목적으로 하는 그리드(grid)가 등장하였다. 이에 본 연구에서는 효율적이면서도 저비용을 갖는 molecular modelling 어플리케이션 개발을 위해 그리드를 기반으로 최적 자원 선택 브로커를 이용하는 molecular docking 어플리케이션을 제안한다. 이를 위해 우리는 molecular docking을 수행하는 그리드 환경의 계층 구조를 설계하고 효율적 작업 수행을 위한 최적 자원 선택 브로커를 설계하였다. 그리고 그리드 환경에서 molecular docking 어플리케이션의 효과적인 수행을 위해 molecular docking 연산 모델을 정의하고 필요한 molecular docking 어플리케이션의 요소들을 설계하였다.

• 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.221-233
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• 2004

Molecular docking falls into the general category of global optimization problems since its main purpose is to find the most stable complex consisting of a receptor and its ligand. Conformational space annealing (CSA), a powerful global optimization method, is incorporated with the Tinker molecular modeling package to perform molecular docking simulations of six receptor-ligand complexes (3PTB, 1ULB, 2CPP, 1STP, 3CPA and 1PPH) from the Protein Data Bank. In parallel, Monte Carlo with minimization (MCM) method is also incorporated into the Tinker package for comparison. The energy function, consisting of electrostatic interactions, van der Waals interactions and torsional energy terms, is calculated using the AMBER94 all-atom empirical force field. Rigid docking simulations for all six complexes and flexible docking simulations for three complexes (1STP, 3CPA and 1PPH) are carried out using the CSA and the MCM methods. The simulation results show that the docking procedures using the CSA method generally find the most stable complexes as well as the native -like complexes more efficiently and accurately than those using the MCM, demonstrating that CSA is a promising search method for molecular docking problems.

• 컴퓨터교육학회논문지
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• 제9권4호
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• pp.63-74
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• 2006

분자 다킹은 신약, 신소재, 고분자의 개발 과정에서 대규모의 화학분자 데이터베이스의 화학분자 데이터들을 실제 실험을 통하지 않고 시뮬레이션을 통해 한정된 화학 분자만을 스크링하는 과정이다. 분자 다킹은 대규모 컴퓨팅 파워와 데이터 저장 용량을 요구하는 대표적인 대규모의 과학 어플리케이션이다. 기존의 분자 다킹 어플리케이션들은 슈퍼컴퓨터, 클러스터, 워크스테이션 등을 이용하여 작업을 수행하도록 개발되었다. 하지만 슈퍼컴퓨터를 이용한 분자 다킹은 너무 많은 비용이 든다는 문제점이 있고, 클러스터나 워크스테이션을 이용한 분자 다킹은 오랜 수행 시간이 요구된다는 문제점을 가지고 있다. 이에 본 논문에서는 그리드 서비스 기반 분자 다킹 어플리케이션을 제안하였다. 이를 위해 본 논문에서는 효율적인 분자 다킹 서비스를 제공하기 위해 자원 브로커와 데이터 브로커를 설계하고, 분자 다킹을 위한 다양한 그리드 서비스들을 개발하였다.

• 통합자연과학논문집
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• 제15권4호
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• pp.179-186
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• 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.

• 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.

• 통합자연과학논문집
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• 제2권2호
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• pp.55-58
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• 2009

A ligand-receptor docking program is an indispensible tool in modern pharmaceutical design. An accurate prediction of small molecular docking pose to a receptor is essential in drug design as well as molecular recognition. An effective docking program requires the ability to locate a correct binding pose in a surprisingly complex conformational space. However, there is an inherent difficulty to predict correct binding pose. The odds are more demanding than finding a needle in a haystack. This mainly comes from the flexibility of both ligand and receptor. Because the searching space to consider is so vast, receptor rigidity has been often applied in docking programs. Even nowadays the receptor may not be considered to be fully flexible although there have been some progress in search algorithm. Improving the efficiency of searching algorithm is still in great demand to explore other applications areas with inherently flexible ligand and/or receptor. In addition to classical search algorithms such as molecular dynamics, Monte Carlo, genetic algorithm and simulated annealing, rather recent algorithms such as tabu search, stochastic tunneling, particle swarm optimizations were also found to be effective. A good search algorithm would require a good balance between exploration and exploitation. It would be a good strategy to combine algorithms already developed. This composite algorithms can be more effective than an individual search algorithms.

• 통합자연과학논문집
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• 제10권3호
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• pp.137-140
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• 2017

Diabetes mellitus has become a major growing public health problem worldwide. More than 90% of all diabetes cases are classified as type 2 diabetes (T2D), which is also known as non-insulin dependent diabetes. Protein tyrosine phosphatase 1B (PTP1B) plays an important role in the negative regulation of insulin signal transduction pathway and has emerged as novel therapeutic strategy for the treatment of type 2 diabetes. PTP1B inhibitors enhance the sensibility of insulin receptor (IR) and have favorable curing effect for insulin resistance-related diseases. Recently twelve anti-diabetic xanthones were isolated from the bark of Garcinia xanthochymus. Hence, in the present study, molecular docking was carried out for these twelve xanthones. The objective of this work is to study the interaction of the newly isolated xanthones with PTP1B. The docking results showed that xanthones have good interactions and has better docking score with PTP1B and suggest LYS120 and ASP181 are the important residues involved in interaction between PTP1B enzyme and the xanthones.

• 통합자연과학논문집
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• 제11권1호
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• pp.25-29
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• 2018

Protein phosphatase manganese dependent 1D (PPM1D), a Ser/Thr protein phosphatise, play major role in the cancer tumorigenesis of various tumors including neuroblastoma, pancreatic adenocarcinoma, medulloblastoma, breast cancer, prostate cancer and ovarian cancer. Hence, analysis on the structural features required for the formation of PPM1D-inhibitor complex becomes essential. In this study, we have performed molecular docking of SL-175 and -176 and protein-protein docking of CDC5L with PPM1D. On analysing the docked complexes, we have identified the important residues involved in the formation of protein-ligand complex. Research concentrating on these residues could be helpful in understanding the pathophysiology of various tumors related to PPM1D.

• 통합자연과학논문집
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• 제9권1호
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• pp.23-27
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• 2016

Hepatitis B virus is the leading source of liver disorders and is a global health problem and needs advancements in its treatment against increasing problems. Recently five vanitaracin derivatives were isolated from the fungus Talaromyces species which have anti-Hepatitis B virus activity. Hence, in the present study, molecular docking was carried out with five vanitaracin derivatives isolated from Talaromyces species and three known inhibitors.The objective of this work is to study the interaction of newly isolated compounds and compare its interaction with known inhibitors. The docking results revealed that vanitaracin derivatives have good interactions and has better docking score with the Hepatitis B virus and suggest SER2, SER4 and ASP30 are important residues involved in interaction with the inhibitors. These result authenticates vanitaracin derivatives contributes to inhibitory activity of Hepatitis B virus to treat liver disorders.

• 통합자연과학논문집
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• 제9권3호
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• pp.161-165
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• 2016

The p21-activated kinase-1 (PAK1) has emerged as a potential target for anticancer therapy. It is overexpressed in ovarian, breast and bladder cancers. This suggests that PAK1 may contribute to tumorigenesis. 4-azaindole derivatives are reported as potent PAK1 inhibitors. The present work deals with the molecular docking studies of 4-azaindoles with PAK1. Probable binding mode of these inhibitors has been identified by molecular modeling. Docking results indicated that hydrogen bonding interactions with Glu345 and Leu347 are responsible for governing inhibitor potency of the compounds. Additionally, Val284, Val328, Met344 and Leu396 were found to be accountable for hydrophobic interactions inside the active site of PAK1.