M. Uebayasi

472 A HIGH PERFORMANCE SYSTEM FOR MOLECULAR DYNAMICS SIMULATION OF BIOMOLECULES USING A SPECIAL-PURPOSE COMPUTER (2009)

Y. Komeiji, H. Yokoyama, M. Uebayasi, M. Taui, T. Fukushige, D. Sugimoto, ...

GRAPE (GRavity PipE) processors are special purpose computers for simulation of classical particles. The performanceof MD-GRAPE, one of the GRAPEs developed for molecular dynamics, was investigated....

Cyclic oxyphosphoranes as model intermediates during splicing and cleavage of RNA: ab initio molecular orbital calculations on the conformational analysis.

Taira, K, Uebayasi, M, Furukawa, K

Ab initio molecular orbital calculations have been carried out on hydrated adducts of methyl ethylene phosphate as a model intermediate during cleavage of RNA. Upon rotating the apical methoxyl group...

Rate limiting P-O(5') bond cleavage of RNA fragment: ab initio molecular orbital calculations on the base-catalyzed hydrolysis of phosphate.

Taira, K, Uchimaru, T, Tanabe, K, Uebayasi, M, Nishikawa, S

In order to examine the energetics in base-catalyzed hydrolysis of RNA, a tentative pentacoordinated intermediate (3) has been characterized by molecular orbital calculations. Ab initio studies at...

Change in conformation by DNA-peptide association: molecular dynamics of the Hin-recombinase-hixL complex.

Komeiji, Y, Uebayasi, M

The Hin-DNA complex is a molecular complex formed by the C-terminal 52mer peptide of the Hin-recombinase and a synthetic 13-bp hixL DNA. The peptide has three alpha-helices, the second and third of...

Cyclic oxyphosphoranes as model intermediates during splicing and cleavage of RNA: ab initio molecular orbital calculations on the conformational analysis.

Taira, K, Uebayasi, M, Furukawa, K

Ab initio molecular orbital calculations have been carried out on hydrated adducts of methyl ethylene phosphate as a model intermediate during cleavage of RNA. Upon rotating the apical methoxyl group...

Rate limiting P-O(5') bond cleavage of RNA fragment: ab initio molecular orbital calculations on the base-catalyzed hydrolysis of phosphate.

Taira, K, Uchimaru, T, Tanabe, K, Uebayasi, M, Nishikawa, S

In order to examine the energetics in base-catalyzed hydrolysis of RNA, a tentative pentacoordinated intermediate (3) has been characterized by molecular orbital calculations. Ab initio studies at...

Change in conformation by DNA-peptide association: molecular dynamics of the Hin-recombinase-hixL complex.

Komeiji, Y, Uebayasi, M

The Hin-DNA complex is a molecular complex formed by the C-terminal 52mer peptide of the Hin-recombinase and a synthetic 13-bp hixL DNA. The peptide has three alpha-helices, the second and third of...