Tomoshi Kameda

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MOTIVATION Understanding the details of protein-RNA interactions is important to reveal the functions of both the RNAs and the proteins. In these interactions, the secondary structures of the RNAs play an important role. Because RNA secondary structures in protein-RNA complexes are variable, considering the ensemble of RNA secondary structures is a useful(More)
Cyclic ADP-ribose (cADPR, 1, Scheme 1), originally isolated from sea urchins by Lee and co-workers, [1] is a general mediator of intracellular Ca 2+ ion signaling. [2] Analogues of cADPR have been extensively designed and synthesized [3, 4] because of their potential usefulness for investigating the mechanisms of cADPR-mediated Ca 2+ release and application(More)
To reduce the number of replicas required in the conventional replica exchange method for huge systems, recently the replica exchange with solute tempering (REST) method was proposed. Here we showed that a variant of REST realized by rescaling the force-field parameters can be performed with GROMACS 4 without changing the code. We tested the variant REST(More)
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