• Bulletin of the Korean Chemical Society
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• v.11 no.4
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• pp.313-317
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• 1990

Geometries for several representative quinolone carboxylate type antibacterials have been calculated by computer graphics/molecular mechanics energy minimization procedures using both MM2 and AMBER force fields. The calculated geometries were found to be in reasonable agreements with the corresponding X-ray crystal structures. It has been pointed out that notwithstanding the weaknesses associated with calculating the resonance and hydrogen bonding contributions, the employed methods are capable of generating credible ring geometries and torsional angle dispositions of N(1)-ethyl and 3-carboxylate substituents of the quinolones.

• Bulletin of the Korean Chemical Society
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• v.10 no.2
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• pp.185-190
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• 1989

Geometries for a number of representative ${\beta}$ -lactam antibiotics (penams, cephems and monobactams) have been calculated by computer graphics/molecular mechanics energy minimization procedures using both MM2 and AMBER force fields. The calculated geometries have been found in reasonable agreement with the geometries reported in the X-ray crystal structures, especially in terms of the pyramidal character of the amide nitrogen in the ${\beta}$-lactam ring and the Cohen distance. Based on these calculations, it is suggested that the nitrogen atom in the monobactams may also have pyramidal geometries in the biologically active conformations.

• Bulletin of the Korean Chemical Society
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• v.10 no.2
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• pp.216-218
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• 1989

• YAKHAK HOEJI
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• v.39 no.1
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• pp.78-84
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• 1995

Based on Computer graphics molecular modeling method, quinolone derivatives as DNA-gyrase inhibitors formed stable DNA-intercalation complex with deoxycytidilyl-3',5'-deoxy guanosine[d($C_{p}G)_{2}$] dinucleotide. When d($C_{p}G)_{2}$ and d($A_{p}T)_{2}$, were compared in order to find out which DNA could form more stable DNA-Drug complex based on interaction energy($\Delta$E) and DNA-Drug complex energy, d($C_{p}G)_{2}$ resulted in lower energy than d($A_{p}T)_{2}$.

• Journal of the Korea Computer Graphics Society
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• v.18 no.3
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• pp.1-7
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• 2012

In this paper, we propose a method to compute the interface between protein molecules. When a molecules is represented as a set of spheres with van der Waals radii, the distance from a spatial point p to the molecule corresponds to the distance from p to the closet sphere. The molecular interface is composed of equi-distant points from two molecules. Our algorithm decomposes the space into a set of voxels, and then constructs a voxel map by storing the information of spheres intersecting each voxel. By using the voxel map, we compute the distance between a point and the molecule. We also use GPU for the parallel processing, and efficiently approximate the interface of a pair of molecules.

• Bulletin of the Korean Chemical Society
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• v.25 no.7
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• pp.1061-1064
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• 2004

Molecular visualization software has the common objective of manipulation and interpretation of data from numerical simulations. They visualize many complicated molecular structures with personal computer and workstation, to help analyze a large quantity of data produced by various computational methods. However, users are often discouraged from using these tools for visualization and analysis due to the difficult and complicated user interface. In this regard, we have developed an easy-to-use three-dimensional molecular visualization and analysis program named POSMOL. This has been developed on the Microsoft Windows platform for the easy and convenient user environment, as a compact program which reads outputs from various computational chemistry software without editing or changing data. The program animates vibration modes which are needed for locating minima and transition states in computational chemistry, draws two and three dimensional (2D and 3D) views of molecular orbitals (including their atomic orbital components and these partial sums) together with molecular systems, measures various geometrical parameters, and edits molecules and molecular structures.

• Bulletin of the Korean Chemical Society
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• v.31 no.12
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• pp.3639-3643
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• 2010

We have developed CUDA-enabled version of a general purpose molecular dynamics simulation code for GPU. Implementation details including parallelization scheme and performance optimization are described. Here we have focused on the non-bonded force calculation because it is most time consuming part in molecular dynamics simulation. Timing results using CUDA-enabled and CPU versions were obtained and compared for a biomolecular system containing 23558 atoms. CUDA-enabled versions were found to be faster than CPU version. This suggests that GPU could be a useful hardware for molecular dynamics simulation.

• Journal of the Korea Computer Graphics Society
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• v.10 no.2
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• pp.1-9
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• 2004

본 논문에서는 바이러스와 같은 생화학 물질의 분자구조를 3 차원 모델로 시각화하여 관찰하고, 그 분자모델을 직관적인 방법으로 조작하기 위한 가상 현실 분자 모델링 시스템을 제안한다. 이 시스템을 사용하면, 입체영상 디스플레이 장치와 데이터 글러브 및 동작 추적 장치를 사용하여 3 차원 분자 모델을 실감나게 조작할 수 있어서 효율적으로 분자들을 관찰하고 결합, 분리하는 등의 분자 모델링 작업이 가능하다. 사용자들은 마우스나 키보드 등의 장비 대신에 자연스러운 몸 동작이나 손 동작을 이용하여 분자 모델링 작업을 위한 동작을 하게 된다. 분자들의 결합을 화학적으로 정확하게, 그리고 실시간으로 시뮬레이션 하기 위해서 에너지 계산 알고리즘을 구현하였으며 이러한 작업이 가능하도록 분자 구조를 표현하는 새로운 자료구조를 제안하였다. 본 연구에서 제안하는 동작 기반의 VR 분자 모델링 시스템의 타당성을 검증하기 위하여 HIV 바이러스 분자를 가지고 분자 모델링 작업을 수행하였고, 사용자 테스트를 실시하여 기존의 방식과 작업 성능 및 사용자 만족도를 비교하였다.

• Journal of the Korea Computer Graphics Society
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• v.14 no.4
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• pp.35-39
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• 2008

A computer supported collaborative system provides with a shared virtual workspace over the Internet where its remote users cooperate in order to achieve their goals by overcoming problems caused by distance and time. VRMMS (Virtual Reality Molecular Modeling System) [1] is a VR based collaborative system where biologists can remotely participate in and exercise molecular modeling tasks such as viewing three dimensional structures of molecular models, confirming results of molecular simulations and providing with feedbacks for the next simulations. Biologists can utilize VRMMS in executing molecular simulations. However, first-time users and beginners need to spend some time for studying and practicing in order to skillfully manipulate molecular models and the system. The best way to resolve the problem is to have a face-to-face session of teaching and learning VRMMS. However, it is not practically recommended in the sense that the users are remotely located. It follows that the learning time could last longer than desired. In this paper, we propose to use Second Life [2] combining with VRMMS for removing the problem. It can be used in building a shared workplace over the Internet where molecular simulations using VRMMS can be exercised, taught, learned and practiced. Through the web, users can collaborate with each other using VRMMS. Their avatars and tools of molecular simulations can be remotely utilized in order to provide with senses of 'being there' to the remote users. The users can discuss, teach and learn over the Internet. The shared workspaces for discussion and education are designed and implemented in Second Life. Since the activities in Second Life and VRMMS are designed to realistic, the system is expected to help users in improving their learning and experimental performances.

• Journal of the Korea Computer Graphics Society
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• v.12 no.2
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• pp.19-25
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• 2006

정보생물학 분야에 있어서 분자 구조를 3차원으로 렌더링하여 보여주는 것은 매우 중요한 작업이다. 특히 분자의 표면 렌더링은 분자의 3차원 구조 분석 등에 중요하게 사용된다. 그러나 분자 표면 렌더링을 수행하기 위해서는 많은 양의 폴리곤이 필요하게 된다. 대장균 바이러스와 같은 분자량이 많은 거대 분자를 자연스럽게 렌더링 하기 위해서는 고성능이며 고가의 그래픽 전용 워크스테이션을 사용해야 한다. 본 논문에서는 PC급 시스템에서도 거대 분자를 무리 없이 렌더링 할 수 있는 효율적인 알고리즘을 제안 하였다. 제안하는 알고리즘은 사용자의 시점에서 최적의 성능 및 시각적인 기여를 할 수 있는 적응형 상세 단계 렌더링을 수행한다. 제안된 알고리즘을 사용하여 거대 분자 모델의 렌더링시 대화식 프레임 수준이상의 성능향상을 보이며, 또한 시각적으로도 분자 모델이 가진 중요한 기하학적인 특성을 유지 할 수 있다.