34 citations · 123 across the 7 of their papers we have counts for
6 papers · 1 filter
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…
Predicting Secondary Structures, Contact Numbers, and Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence by Critical Random Networks
Akira R. Kinjo, Ken Nishikawa
Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the und…
Predicting Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence
Akira R. Kinjo, Ken Nishikawa
Residue-wise contact order (RWCO) is a new kind of one-dimensional protein structures which represents the extent of long-range contacts. We have recently shown that a set of three…
Recoverable One-dimensional Encoding of Three-dimensional Protein Structures
Akira R. Kinjo, Ken Nishikawa
Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a…