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Journal Articles

Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction

Ikebe, Kimiyoshi; Umezawa, Koji*; Higo, Junichi*

Biophysical Reviews, 8(1), p.45 - 62, 2016/03

Journal Articles

H3 histone tail conformation within the nucleosome and the impact of K14 acetylation studied using enhanced sampling simulation

Ikebe, Kimiyoshi; Sakuraba, Shun*; Kono, Hidetoshi

PLOS Computational Biology, 12(3), p.e1004788_1 - e1004788_13, 2016/03

 Times Cited Count:31 Percentile:91.07(Biochemical Research Methods)

Journal Articles

Adaptive lambda square dynamics simulation; An Efficient conformational sampling method for biomolecules

Ikebe, Kimiyoshi; Sakuraba, Shun; Kono, Hidetoshi

Journal of Computational Chemistry, 35(1), p.39 - 50, 2014/01

 Times Cited Count:14 Percentile:45.64(Chemistry, Multidisciplinary)

Oral presentation

Conformational search of an H3 histone tail by using partial multicanonical MD

Ikebe, Kimiyoshi

no journal, , 

DNA in eukaryotic cells is folded into a compact chromatin structure and stored in a nucleus. However, the chromatin is deformed when the DNA should work. The mechanism of the chromatin de- and re-formation is important for DNA functional regulation and it is noted that it is controlled by chemical modifications to histone tails, which is one of components of a chromatin. In the current study, I try to elucidate the mechanism by reproducing a state of an H3 histone tail, which is a kind of histone tails and has large conformational fluctuation, with a simulation technique, partial McMD. In this presentation, I first introduce about an importance of the histone tail study and partial McMD. Then, we explain a controversial point of partial McMD.

Oral presentation

Conformational sampling of a H3 histone tail in a nucleosome

Ikebe, Kimiyoshi; Kono, Hidetoshi

no journal, , 

no abstracts in English

Oral presentation

Free energy profile for nucleosomal DNA unwrapping

Kono, Hidetoshi; Yonetani, Yoshiteru; Ikebe, Kimiyoshi; Sakuraba, Shun; Ishida, Hisashi

no journal, , 

Oral presentation

Oral presentation

Oral presentation

Conformational sampling of a histone tail with ALSD simulation

Ikebe, Kimiyoshi; Sakuraba, Shun; Kono, Hidetoshi

no journal, , 

no abstracts in English

Oral presentation

Conformational sampling simulation of an H3 histone tail by Adaptive Lambda Square Dynamics method

Ikebe, Kimiyoshi; Sakuraba, Shun; Kono, Hidetoshi

no journal, , 

no abstracts in English

Oral presentation

Structure and dynamics of histone H$$_{3}$$ tail

Kono, Hidetoshi; Ikebe, Kimiyoshi

no journal, , 

no abstracts in English

Oral presentation

Structural ensemble of H3 histone tail in mono-nucleosome

Kono, Hidetoshi; Ikebe, Kimiyoshi

no journal, , 

no abstracts in English

Oral presentation

How does an acetylation on a histone tail affect the conformation

Ikebe, Kimiyoshi; Sakuraba, Shun; Kono, Hidetoshi

no journal, , 

no abstracts in English

Oral presentation

How does an acetylation on a histone tail affect the conformation ?

Ikebe, Kimiyoshi; Sakuraba, Shun; Kono, Hidetoshi

no journal, , 

no abstracts in English

Oral presentation

How does an acetylation affect conformation of an H3 histone tail?

Ikebe, Kimiyoshi; Sakuraba, Shun*; Kono, Hidetoshi

no journal, , 

Oral presentation

Dynamics of nucleosomes and impact of acetylation

Kono, Hidetoshi; Ikebe, Kimiyoshi; Sakuraba, Shun*; Ishida, Hisashi

no journal, , 

Oral presentation

How does an acetylation affect the conformation of H3 histone tail ?

Ikebe, Kimiyoshi; Sakuraba, Shun*; Kono, Hidetoshi

no journal, , 

26 (Records 1-20 displayed on this page)