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Prediction of parathyroid hormone signalling potency using SVMs
Yoo, Ahrim,Ko, Sunggeon,Lim, Sung-Kil,Lee, Weontae,Yang, Dae Ryook Springer-Verlag 2009 Molecules and cells Vol.27 No.5
<P>Parathyroid hormone is the most important endocrine regulator of calcium concentration. Its N-terminal fragment (1-34) has sufficient activity for biological function. Recently, site-directed mutagenesis studies demonstrated that substitutions at several positions within shorter analogues (1-14) can enhance the bioactivity to greater than that of PTH (1-34). However, designing the optimal sequence combination is not simple due to complex combinatorial problems. In this study, support vector machines were introduced to predict the biological activity of modified PTH (1-14) analogues using mono-substituted experimental data and to analyze the key physicochemical properties at each position that correlated with bioactivity. This systematic approach can reduce the time and effort needed to obtain desirable molecules by bench experiments and provide useful information in the design of simpler activating molecules.</P>
Prediction of Parathyroid Hormone Signalling Potency Using SVMs
Ahrim Yoo,고성건,임승길,이원태,양대륙 한국분자세포생물학회 2009 Molecules and cells Vol.27 No.5
Parathyroid hormone is the most important endocrine regulator of calcium concentration. Its N-terminal fragment (1-34) has sufficient activity for biological function. Recently, site-directed mutagenesis studies demonstrated that substitutions at several positions within shorter analogues (1-14) can enhance the bioactivity to greater than that of PTH (1-34). However, designing the optimal sequence combination is not simple due to complex combinatorial problems. In this study, support vector machines were introduced to predict the biological activity of modified PTH (1-14) analogues using mono-substituted experimental data and to analyze the key physicochemical properties at each position that correlated with bioactivity. This systematic approach can reduce the time and effort needed to obtain desirable molecules by bench experiments and provide useful information in the design of simpler activating molecules.
Predicting the Three-Dimensional Structures of Proteins: Combined Alignment Approach
Jaehyun Sim,Jooyoung Lee,Ahrim Yoo,Seung-Yeon Kim 한국물리학회 2004 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.44 No.32
Protein structure prediction is a great challenge in molecular biophysics and bioinformatics. Most approaches to structure prediction use known structure information from the Protein Data Bank (PDB). In these approaches, it is most crucial to nd a homologous protein (template) from the PDB to a query sequence and to align the query sequence to the template sequence. We propose a prole-prole alignment method based on the cosine similarity criterion, and combine this with a sequence-prole alignment, the secondary structure prediction of the query protein, and the experimental secondary structure of the template protein. Our method, which we call combined alignment, provides good results for the 1107 query-template pairs of the SCOP database and the CASP5 target proteins. They show that combined alignment signicantly improves the recognition of distant homology.