155 citations · 404 across the 20 of their papers we have counts for
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Similarity search for local protein structures at atomic resolution by exploiting a database management system
Akira R. Kinjo, Haruki Nakamura
A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a…
Nature of protein family signatures: Insights from singular value analysis of position-specific scoring matrices
Akira R. Kinjo, Haruki Nakamura
Position-specific scoring matrices (PSSMs) are useful for detecting weak homology in protein sequence analysis, and they are thought to contain some essential signatures of the pro…
On the optimal contact potential of proteins
Akira R. Kinjo, Sanzo Miyazawa
We analytically derive the lower bound of the total conformational energy of a protein structure by assuming that the total conformational energy is well approximated by the sum of…
Wang-Landau molecular dynamics technique to search for low-energy conformational space of proteins
Takehiro Nagasima, Akira R. Kinjo, Takashi Mitsui +1
Multicanonical molecular dynamics (MD) is a powerful technique for sampling conformations on rugged potential surfaces such as protein. However, it is notoriously difficult to esti…