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The FALC-Loop web server for protein loop modeling
Ko, Junsu,Lee, Dongseon,Park, Hahnbeom,Coutsias, Evangelos A.,Lee, Julian,Seok, Chaok Oxford University Press 2011 Nucleic acids research Vol.39 No.2
<P>The FALC-Loop web server provides an online interface for protein loop modeling by employing an <I>ab initio</I> loop modeling method called FALC (fragment assembly and analytical loop closure). The server may be used to construct loop regions in homology modeling, to refine unreliable loop regions in experimental structures or to model segments of designed sequences. The FALC method is computationally less expensive than typical <I>ab initio</I> methods because the conformational search space is effectively reduced by the use of fragments derived from a structure database. The analytical loop closure algorithm allows efficient search for loop conformations that fit into the protein framework starting from the fragment-assembled structures. The FALC method shows prediction accuracy comparable to other state-of-the-art loop modeling methods. Top-ranked model structures can be visualized on the web server, and an ensemble of loop structures can be downloaded for further analysis. The web server can be freely accessed at http://falc-loop.seoklab.org/.</P>
GalaxyWEB server for protein structure prediction and refinement
Ko, Junsu,Park, Hahnbeom,Heo, Lim,Seok, Chaok Oxford University Press 2012 Nucleic acids research Vol.40 No.w1
<P>Three-dimensional protein structures provide invaluable information for understanding and regulating biological functions of proteins. The GalaxyWEB server predicts protein structure from sequence by template-based modeling and refines loop or terminus regions by <I>ab initio</I> modeling. This web server is based on the method tested in CASP9 (9th Critical Assessment of techniques for protein Structure Prediction) as ‘Seok-server’, which was assessed to be among top performing template-based modeling servers. The method generates reliable core structures from multiple templates and re-builds unreliable loops or termini by using an optimization-based refinement method. In addition to structure prediction, a user can also submit a refinement only job by providing a starting model structure and locations of loops or termini to refine. The web server can be freely accessed at http://galaxy.seoklab.org/.</P>
GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions
Ko, Junsu,Park, Hahnbeom,Seok, Chaok BioMed Central 2012 BMC bioinformatics Vol.13 No.-
<P><B>Background</B></P><P>Protein structures can be reliably predicted by template-based modeling (TBM) when experimental structures of homologous proteins are available. However, it is challenging to obtain structures more accurate than the single best templates by either combining information from multiple templates or by modeling regions that vary among templates or are not covered by any templates.</P><P><B>Results</B></P><P>We introduce GalaxyTBM, a new TBM method in which the more reliable core region is modeled first from multiple templates and less reliable, variable local regions, such as loops or termini, are then detected and re-modeled by an <I>ab initio</I> method. This TBM method is based on “Seok-server,” which was tested in CASP9 and assessed to be amongst the top TBM servers. The accuracy of the initial core modeling is enhanced by focusing on more conserved regions in the multiple-template selection and multiple sequence alignment stages. Additional improvement is achieved by <I>ab initio</I> modeling of up to 3 unreliable local regions in the fixed framework of the core structure. Overall, GalaxyTBM reproduced the performance of Seok-server, with GalaxyTBM and Seok-server resulting in average GDT-TS of 68.1 and 68.4, respectively, when tested on 68 single-domain CASP9 TBM targets. For application to multi-domain proteins, GalaxyTBM must be combined with domain-splitting methods.</P><P><B>Conclusion</B></P><P>Application of GalaxyTBM to CASP9 targets demonstrates that accurate protein structure prediction is possible by use of a multiple-template-based approach, and <I>ab initio</I> modeling of variable regions can further enhance the model quality.</P>
Ko, Seunghwan,Lee, Junsu,Koo, Joonhoi,Joo, Beom Soo,Gu, Minseon,Lee, Ju Han IEEE 2016 Journal of Lightwave Technology Vol.34 No.16
<P>We propose a chemical wet etching technique that does not make use of toxic Hydrofluoric solution to produce cladding-etched optical fiber intended for use as a platform for a fiberized saturable absorber. The wet etching technique is based on the use of a mixed solution of NH4F and (NH4)(2)SO4, which is not toxic, and a small, specially-devised etching cradle to achieve precise control of the etched fiber length. A fiberized saturable absorber was implemented by depositing the graphene oxide particles on top of the residual cladding for our cladding-etched fiber by using the drop & dry method. The saturable absorber was incorporated into an erbium-doped fiber ring cavity to test its suitability as a mode-locker with a modulation depth larger than 4.3%. Femtosecond pulses with a temporal width of similar to 615 fs were readily obtained at a repetition rate of similar to 17.09 MHz. The saturable absorption and laser performance of our saturable absorber were compared to those of an absorber on a core-etched fiber platform prepared through the formation of microdroplets of HF and surface tension-driven flow, as in [57].</P>
액체로켓엔진 산화제(과산화수소) 공급계 구축에 관한 연구
전준수(Junsu Jeon),정재훈(Jaehoon Jeong),김유(Yoo Kim),고영성(Youngsung Ko),김선진(Sunjin Kim) 한국추진공학회 2009 한국추진공학회 학술대회논문집 Vol.2009 No.5
본 연구에서는 액체로켓엔진 산화제로 과산화수소를 사용하기 위한 공급 설비 구축 및 세척 방법을 제시하고자 한다. 과산화수소 공급 설비의 오염을 최소화하기 위하여 공급 설비를 세척하고 세척된 공급 설비에 보호막을 입히는 passivation 절차를 확립하였다. 또한, 구축된 공급 설비는 누설 시험과 연소 시험을 통해서 안정성을 검증하였다. This study suggests manufacturing and cleaning the feeding system of hydrogen peroxide to use oxidizer of liquid rocket. We established the process of cleaning and passivation in order to minimize the pollution of Hydrogen Peroxide feeding system. And, we verified stability of the manufactured feeding system by leak test & hot test.
친환경 추진제를 사용하는 저추력 엑체로켓엔진의 혼합비에 따른 연소 특성
전준수(Junsu Jeon),김영문(Youngmun Kim),황오식(Osik Hwang),고영성(Youngsung Ko),김유(Yoo Kim),김선진(Sunjin Kim) 한국추진공학회 2009 한국추진공학회 학술대회논문집 Vol.2009 No.11
본 연구에서는 친환경 추진제인 고농도 과산화수소와 케로신을 사용하는 저추력 이원추진제 로켓 엔진의 O/F ratio에 따른 연소 성능 특성을 파악하였다. 연소시험에 사용된 엔진은 6개의 동축 스월 인젝터로 구성된 멀티 인젝터와 연소실, 노즐로 구성되어있으며, 촉매 점화 방식을 사용하였다. 연소 시험은 O/F ratio 3.8에서 11.0까지 변화시켜가며 수행하였다. 연소 시험 결과를 이용하여 특성 속도(C<SUP>*</SUP>)와 압력 섭동 값을 계산한 결과, 연소 효율은 O/F ratio 5~6 구간에서 가장 좋았으며 모든 구간에서 연소실 압력대비 압력 섭동 값이 5% 미만으로 안정적임을 확인하였다. Combustion tests of a low thrust rocket engine was performed to get combustion characteristics, which used a high concentrated hydrogen peroxide and kerosene as the oxidizer and fuel. The engine consisted of multi injector(six coaxial swirl injectors), chamber, nozzle and catalyst ignition system. The test was carried out by changing O/F ratio from 3.8 to 11.0. The experimental results showed that combustion efficiency was highest at O/F ratio from 5 to 6 and pressure fluctuations of all the range were lower than 5%.