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Ryu, Hyojung,Lim, GyuTae,Sung, Bong Hyun,Lee, Jinhyuk Oxford University Press 2016 Bioinformatics Vol. No.
<P><B>Summary:</B> Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a web-based server for NMR structure refinement. The previously developed knowledge-based energy function STAP (Statistical Torsion Angle Potential) was used for NMRe refinement. With STAP, NMRe provides two refinement protocols using two types of distance restraints. If a user provides NOE (Nuclear Overhauser Effect) data, the refinement is performed with the NOE distance restraints as a conventional NMR structure refinement. Additionally, NMRe generates NOE-like distance restraints based on the inter-hydrogen distances derived from the input structure. The efficiency of NMRe refinement was validated on 20 NMR structures. Most of the quality assessment scores of the refined NMR structures were better than those of the original structures. The refinement results are provided as a three-dimensional structure view, a secondary structure scheme, and numerical and graphical structure validation scores.</P><P><B>Availability and implementation:</B> NMRe is available at http://psb.kobic.re.kr/nmre/</P><P><B>Contact:</B> jinhyuk@kribb.re.kr</P><P><B>Supplementary information:</B> Supplementary data are available at <I>Bioinformatics</I> online.</P>
NMR Structure Determination by Conformational Space Annealing
Jinhyuk Lee,Jinwoo Lee,Jooyoung Lee 한국산업응용수학회 2009 한국산업응용수학회 학술대회 논문집 Vol.4 No.2
We have carried out numerical experiments to investigate the applicability of global optimization method to the NMR structure determination. Since the number of NMR observables is relatively small in the early stage of NMR structure determination process and long range NOE observables are difficult to obtain, advanced sampling techniques are greatly in need to generate valid NMR structures from a small number of experimental restraints. By utilizing conformational space annealing method, we have determined solution NMR structures from NOE distance and backbone dihedral restraints. Several solution NMR structures are determined starting from fully randomized conformations. We have evaluated them by measuring the qualities of determined structures, such as structure convergence of ensemble, Ramachandran preferences, clash scores, and the total NOE violation. These qualities are compared to those from the corresponding PDB structures.
Sulfuretin, a natural Src family kinases inhibitor for suppressing solar UV-induced skin aging
Han, Ahram,Lee, Jinhyuk,Lee, Myung-hee,Lee, Sung-Young,Shin, Eun Ju,Song, Young-Ran,Lee, Kwang Min,Lee, Ki Won,Lim, Tae-Gyu Elsevier 2019 Journal of Functional Foods Vol.52 No.-
<P><B>Abstract</B></P> <P>This study suggests sulfuretin as an ant-skin aging agent. Sulfuretin significantly reduces solar UV (sUV)-increased matrix metalloproteinase-1 (MMP-1) expression and c-Jun phosphorylation in human dermal fibroblasts as well as skin tissue. An examination of the underlying mechanisms showed that sUV-activated MAPK signaling pathways are blocked by sulfuretin. Interestingly, sulfuretin directly inhibits the kinase activity of selected Src family. Because the amino acid sequence of Hck kinase which used kinase array is 230–497, it was assumed that sulfuretin interacts with this conserved domain of Src family kinase. It was also found that sulfuretin directly binds to sulfuretin with the lowest binding energy of −8.9 kcal/mol and free energy of −10.07 kcal/mol. Additionally, Hck protein was precipitated with sulfuretin-conjugated Sepharose 4B beads in HDFs cell lysate. Overall, present findings indicated that sulfuretin plays the role of anti-skin aging agent by acting as a general Src family kinase inhibitor in human skin.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The anti-wrinkle formation activity of sulfuretin was suggested. </LI> <LI> Sulfuretin acts as general Src family kinase inhibitor. </LI> <LI> The expected interaction was assumed using computer modeling. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>
Vision-based Tactile Sensor using Random Pattern
Jinhyuk Lee,Suwoong Lee,Minyoung Kim 제어로봇시스템학회 2022 제어로봇시스템학회 국제학술대회 논문집 Vol.2022 No.11
Tactile sensors are being used in various fields such as automated factories and human collaboration, and have been developed in various technological ways. Most contact discrimination methods are performed through sensing of the physical aspect. On the other hand, in recent years, a vision-based tactile sensor that can obtain more information by replacing the existing method with only visual data of an image using a camera sensor has been proposed. Existing visionbased tactile sensors have markers as a standard to detect changes or have a pattern of a certain shape and arrangement. We propose a vision-based tactile sensor that can estimate the position of a contact with an easy design and compact hardware size. As a vision-based tactile sensor is a sensor that acquires various information about contact through image processing of visual data, it is possible to update the function of a tactile sensor by making good use of the fact that it is possible only through algorithm development without a separate hardware reconfiguration. We plan to continue our research to obtain more detailed contact information such as accuracy, force, and direction of force.