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조광휘,Poul Erik Hansen 대한화학회 2020 Bulletin of the Korean Chemical Society Vol.41 No.1
A simple method is suggested to identify the structure of novel compounds with basic IR, 1H, and 13C nuclear magnetic resonance (NMR) spectroscopy and computational tools. With the molecular formula obtained from high-resolution mass spectrometry, all possible isomers are calculated. The absence or presence of particular functional groups which were inferred from IR, 1H, and 13C NMR and DEPT spectra are used to sort all the possible isomers using SMARTS code and RDKit. Then, the final structure(s) are identified by comparing the correlation between Quantum mechanically calculated 13C NMR chemical shielding constants and experimental 13C chemical shifts of molecules in consideration. We have applied this protocol to five natural compounds, the number of heavy atoms ranging from 11 to 15, and correctly identified the structures of all test cases. The limitations and further consideration are discussed.
조광휘,주상우 대한화학회 2008 Bulletin of the Korean Chemical Society Vol.29 No.1
Tautomerism of pyrimidine base cytosine has been comparatively examined on nanoparticle and roughened plate surfaces of silver, gold, and copper by surface-enhanced Raman scattering (SERS). The SERS spectrum was found to be different depending on the metals and their substrate conditions suggesting the dissimilar population of various tautomers of cytosine on the surfaces. The ab initio calculations were performed at the levels of B3LYP, HF, and MP2 levels of theory with the LanL2DZ basis set to estimate the energetic stability of the tautomers with the metal complexes as well as the gas phase state. The amino group and N3-coordinated tautomer was predicted to be more favorable for bonding to Au, whereas the hydroxyl and N1-coordinated zwitter ionic form is most stable with Ag and Cu as a bidentate form from the DFT calculation. The binding energy with the Ag atom is calculated to be smaller than those with the Au and Cu atoms in line with the temperature-dependent SERS spectra of cytosine.
PyQSAR: A Fast QSAR Modeling Platform Using Machine Learning and Jupyter Notebook
김신영,조광휘 대한화학회 2019 Bulletin of the Korean Chemical Society Vol.40 No.1
Understanding the relationship between structure and property is important in current research works. The QSAR/QSPR (Quantitative Structure?Activity Relationship/Quantitative Structure?Property Relationship) is a common method for finding the relationships between the structure and property of compounds. However, traditional methods of performing QSAR analysis rely on multiple software platforms for each step. Here, an integrated standalone python package, PyQSAR, is proposed that combines all QSAR modeling process in one workbench. The efficiency of the package was verified by comparing to 10 previously published works. The results showed high performance of PyQSAR in terms of R 2 with less than half an hour execution time with a typical desktop PC for each test case. The main goal of PyQSAR is the production of reliable QSAR models on a single platform with an easy-to-follow workflow.
Protein Structure Prediction Using a Hybrid Energy Function and an Exact Enumeration
이주련,조광휘 한국물리학회 2008 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.53 No.2
We develop a protein structure prediction method that utilizes fragment assembly and a hybrid energy function. In a fragment assembly method, the local structure of the backbone is obtained from a structural database by using similarity of sequence features, in contrast to a pure physicsbased method in which all dihedral angles are allowed to vary continuously. Since the conformational space for the backbone is finite, we generate all possible conformations and vary only the side-chain dihedral angles for each of them. The conformations are scored using a hybrid energy function, where all the backbone atoms are described explicitly, but the side chain is modeled as a few interaction centers. We perform a test prediction on four proteins, 1l2y, 1e0l, 1bdd and 1bk2, to demonstrate the feasibility of protein structure prediction based on exact enumeration.
구남진,조광휘,Gu, Nam-Jin,Jo, Gwang-Hwi 한국생물정보시스템생물학회 2007 Bioinformatics and Biosystems Vol.2 No.1
Short interfering RNA(siRNA)는 특별한 gene의 발현을 막는데 사용될 수 있고 그 gene의 기능과 치료의 적용에 많은 가능성을 가지고 있지만, 효과적인 siRNA를 디자인하는 방법은 아직까지 명확하지 않다. 효과적인 siRNA는 서열적인 경향을 가지고 있는데 낮은 G/C content, Sense strand의 3' 끝에 적은 안정성과 1번 위치에는 G/C, 19번 위치에는 A/U의 존재 여부를 들 수 있다. 이러한 특성 말고도 최근에는 mRNA의 2차구조가 RNAi 작용에 중요한 역할을 하게 되는데 복잡한 구조(hairpin, multi loop)를 가지고 수소결합을 많이 하여 안정한 상태에 있는 부분은 siRNA의 기능을 크게 줄어들게 한다. 또한, siRNA가 특정한 mRNA에 작동하도록 BLAST 검색을 하여 부작용의 가능성을 배제한다. Shot interfering RNA (siRNA) can be used to silence specific gene expression and have many potential therapeutic applications. However, how to design an effective siRNA is still not clear. Highly effective siRNA has sequence-specific properties which are low G/C content, low internal stability at the sense strand 3'-terminus, sense strand base bias(position 1 is G/C, position 19 is /AU). Recently, mRNA secondary structure playsan important role in RNAi. Target site of siRNA in high-ordered structure (i.e hairpin loop, multi loop) or base pair of many hydrogen bonds dramatically reduce function of siRNA mediated gene silencing. Possible off-target effects of siRNA is detecting from BLAST search.