Kazuyoshi Ikeda

Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces (2008)

Ikeda, Kazuyoshi, Hirokawa, Takatsugu, Higo, Junichi, Tomii, Kentaro

Abstract Background Many studies have examined rules governing two aspects of protein structures: short segments and proteins' structural domains. Nevertheless, the organization and nature of the...

An integrative in silicoapproach for discovering candidates for drug-targetable protein-protein interactions in interactome data (2007)

Sugaya, Nobuyoshi, Ikeda, Kazuyoshi, Tashiro, Toshiyuki, Takeda, Shizu, Otomo, Jun, Ishida, Yoshiko, ...

Abstract Background Protein-protein interactions (PPIs) are challenging but attractive targets for small chemical drugs. Whole PPIs, called the 'interactome', have been emerged in several organisms,...

Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs

Ikeda, Kazuyoshi, Tomii, Kentaro, Yokomizo, Tsuyoshi, Mitomo, Daisuke, Maruyama, Keiichiro, Suzuki, Shinya, ...

Analysis of the conformational distribution of polypeptide segments in a conformational space is the first step for understanding a principle of structural diversity of proteins. Here, we present a...

Free-energy landscape of a chameleon sequence in explicit water and its inherent α/β bifacial property

Ikeda, Kazuyoshi, Higo, Junichi

A sequence in yeast MATα2/MCM1/DNA complex that folds into α-helix or β-hairpin depending on the surroundings has been known as "chameleon" sequence. We obtained the free-energy landscape of this...