Nagasima, Takehiro, Kinjo, Akira R., Mitsui, Takashi, Nishikawa, Ken
Multicanonical molecular dynamics (MD) is a powerful technique for sampling conformations on rugged potential surfaces such as protein. However, it is notoriously difficult to estimate the...
Homma, Keiichi, Fukuchi, Satoshi, Nakamura, Yoji, Gojobori, Takashi, Nishikawa, Ken
The formation mechanism of operons remains controversial despite the proposal of many models. Although acquisition of genes from other species, horizontal gene transfer, is considered to occur,...
Kinjo, Akira R, Nishikawa, Ken
Abstract Background One-dimensional protein structures such as secondary structures or contact numbers are useful for three-dimensional structure prediction and helpful for intuitive understanding of...
Kinjo, Akira R., Nishikawa, Ken
Background: One-dimensional protein structures such as secondary structures or contact numbers are useful for three-dimensional structure prediction and helpful for intuitive understanding of the...
Homma, Keiichi, Fukuchi, Satoshi, Nakamura, Yoji, Gojobori, Takashi, Nishikawa, Ken
This paper was withdrawn by the authors.
Kinjo, Akira R., Nishikawa, Ken
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 understanding of...
Predicting Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence (2005)
Kinjo, Akira R., Nishikawa, Ken
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 types of...
Recoverable One-dimensional Encoding of Three-dimensional Protein Structures (2005)
Kinjo, Akira R., Nishikawa, Ken
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 protein is encoded...
Genome Informatics 14: 468--469 (2003) Estimation of the Number of Orphan Genes in the (2004)
Satoshi Fukuchi, Ken Nishikawa
Introduction In annotations of genome sequences a considerable fraction of putative proteins are left without sequence similarity to known proteins. These genes or open reading frames (ORFs) have...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
An international team has systematically validated and annotated just over 21,000 human genes using full-length cDNA, thereby providing a valuable new resource for the human genetics community.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Motonori Ota, Ken Nishikawa, Tatsuo Ooi
occus jannaschii, Archaeoglobus fulgidus, and Saccharomyces cerevisiae have been investigated [2]. The dinucleotide composition was significantly differentbetween the organisms. The distribution of...
protein was excluded in the analysis. Membrane proteins were excluded from the analysis. We prepared two sets of sequence data, one was a training set to determine a parameter set of score and the...
GTOP: a database of protein structures predicted from genome sequences
Kawabata, Takeshi, Fukuchi, Satoshi, Homma, Keiichi, Ota, Motonori, Araki, Jiro, Ito, Takehiko, ...
Large-scale genome projects generate an unprecedented number of protein sequences, most of them are experimentally uncharacterized. Predicting the 3D structures of sequences provides important clues...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Ohta, Takeshi, Kawabata, Takeshi, Nishikawa, Ken, Tani, Akio, Kimbara, Kazuhide, Kawai, Fusako
Polyethylene glycol dehydrogenase (PEGDH) from Sphingopyxis terrae (formerly Sphingomonas terrae) is composed of 535 amino acid residues and one flavin adenine dinucleotide per monomer protein in a...
GTOP: a database of protein structures predicted from genome sequences
Kawabata, Takeshi, Fukuchi, Satoshi, Homma, Keiichi, Ota, Motonori, Araki, Jiro, Ito, Takehiko, ...
Large-scale genome projects generate an unprecedented number of protein sequences, most of them are experimentally uncharacterized. Predicting the 3D structures of sequences provides important clues...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Ohta, Takeshi, Kawabata, Takeshi, Nishikawa, Ken, Tani, Akio, Kimbara, Kazuhide, Kawai, Fusako
Polyethylene glycol dehydrogenase (PEGDH) from Sphingopyxis terrae (formerly Sphingomonas terrae) is composed of 535 amino acid residues and one flavin adenine dinucleotide per monomer protein in a...