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Profile-based Nearest Neighbor Method for Pattern Recognition
주기형,Jooyoung Lee,Ilsoo Kim,Julian Lee,Seung-Yeon Kim,Sung Jong Lee 한국물리학회 2004 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.44 No.32
We propose a nearest neighbor method of pattern recognition which is based on a weighted distance measure between patterns derived from proles. There are a few new ingredients to the proposed method, compared to the conventional nearest neighbor methods. The distance measure is dened as a weighted sum of each pattern component, and the weight parameters are optimized. We introduce a second-layer prediction procedure analogous to that in neural network methods. We rst construct a pattern database, where the classication of each pattern is already known. Prediction for a query pattern is performed by examining patterns close to it. We apply the proposed method to predict the protein secondary structure of the proteins in the CB513 set and 29 proteins from CASP5 in blind fashion. We nd that the performance of our approach, especially with the second-layer prediction, is almost comparable to the state-of-the-art method based on neural network methods.
주기형,김미선,박지민,이주영,신동해 한국구조생물학회 2015 Biodesign Vol.3 No.3
We have solved the crystal structures of predicted fructose-specific enzyme IIBfruc from Escherichia coli (EcEIIBfruc) andD-glycero-D-manno-heptose-1,7-bisphosphate phosphatase from Burkholderia thailandensis (BtGmhB) of which the X-raydata contain various crystallographic problems. The bottleneck of the structural determination by X-ray crystallographywas the phasing of the diffraction data. The obstacles were overcome by molecular replacement (MR) using the GOT(Global-Optimization-based Template-based modeling of proteins) models combined with the exhaustive search by bruteforceautomation of phasing trials. This study suggests that the current computational approach can be applied to manyunsolved MR problems where better 3D protein models are required or/and the MR solution is limited by the ambiguity inthe crystallographic data.
Single-chain insulin analogs as an insulin agonist and their implications for receptor binding
신동호,주기형,이주영,신항철 한국구조생물학회 2015 Biodesign Vol.3 No.4
The importance of conformational change has recently become a focus for considering the mechanisms by whichinsulin and its receptor combine to achieve an effective ligand-receptor complex. Although the insulin structure boundto its receptor (active structure) is still unknown, there are evidences that conformational change takes place in thecarboxy terminal region of the insulin B-chain on receptor binding. In the present study, we have produced varioussingle-chain insulin analogs where C-terminus of B-chain and N-terminus of A-chain are connected by various shortpeptides. Significant increase of bioactivity was noticed when two pairs of dibasic residues were included as part of theconnecting peptide, indicating that the distance between C-terminus of B-chain and N-terminus of A-chain changes dueto the repulsive force between RR and KR residues, probably further apart than without the RR and KR residues. Proteinmodeling suggests that insulin and single-chain insulin analogs need to open up their receptor-binding pockets for theiractivities. The development of highly active single-chain insulin analog may facilitate the design of novel insulin analogs ornon-peptide alternatives.
단백질 3차 구조 모델링에 기반한 리간드 결합부위 예측
오민아(Oh Mina),주기형,이주영 한국산업응용수학회 2009 한국산업응용수학회 학술대회 논문집 Vol.4 No.2
단백질 구조 및 리간드 (ligand) 결합부위에 대한 정보는 단백질 기능을 이해하는데 중요한 가이드 역할을 한다. 본 연구에서는 리간드 결합부위 예측을 위해 크게 두 단계의 계산이 수행되었다. (1) 아미노산 서열로부터 템플릿 기반 모델링 방법을 사용, 단백질의 3차 구조가 예측되었다. (2) 단백질 구조 예측에 사용된 단백질-리간드 복합체 구조를 이용, 예측된 단백질 모델로부터 단백질-리간드 결합부위를 예측하였다. 이 방법은 27개 CASP8 기능 예측 단백질에 대해서 적용 되었고, Accuracy=70, Coverage=80의 우수한 결과를 냈다. 특히, 단백질-리간드 결합부위의 예측에 사용된 단백질 모델 대신에 실험에 의해 결정된 native 구조를 사용했을 경우 그 결과에서 큰 차이를 보이지 않았다. 단백질-리간드 결합부위 예측은 리간드에 대한 정보 없이 수행되었는데, 많은 경우에 실재로 native에서 결합하는 리간드는 상이했음에도 불구하고 본 연구의 접근방법은 성공적이었다.
정희찬(Heechan Jeong),최성무(Sungmu Choi),서정민(Jungmin Seo),주기형(Kihyeong Joo) 한국자동차공학회 2015 한국자동차공학회 부문종합 학술대회 Vol.2015 No.5
White smoke from the diesel vehicles with DPF using high sulfur fuel (> 50 ppm) are not being selling up to now. The emerging markets like BRIC’s are using quite stringent emission regulations like EU4 and EU5. But their fuel qualities are not higher than their emission regulation. Their poor fuel qualities are preventing car makers from using DPF system to reduce particulate matter. To prevent emitting white smoke and meet EU4 and EU5 emission regulation with DPF in these countries that have poor fuel quality, DOC+DPF system that suppresses white smoke was newly developed. Based on this development, DOC+DPF system that meets Chinese emission regulation like KUK 4 and KUK 5 or India emission regulation like BS4 and BS5 were developed and the mechanism of white smoke was also investigated. By applying this white smoke suppression system, diesel vehicle with DPF can be sold in BRIC’s market. Therefore it is expected that this DOC+DPF that suppresses white smoke can contribute to increasing sales of diesel vehicles in BRIC’s market a lot.