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http://daisy.bio.nagoya-u.ac.jp/golab/hetpdbnavi.html
Yamaguchi, A.1, Tomoda, S.2, Yura, K.3, Go, M.1
1Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, JAPAN
2Faculty of Science and Technology, Hirosaki University, Hirosaki 036-8560, JAPAN
3Quantum Bioinformatics Group, Japan Atomic Energy Research Institute, 8-1 Umemidai, Kizu, Souraku, Kyoto 619-0215, JAPAN
Contact go@bio.nagoya-u.ac.jp
Het-PDB Navi. is a database that collects small molecules found in Protein Data Bank (PDB). The database aims to help function annotations of open reading frames gained from genome sequencing projects. An atomic reality of protein function is based on interactions between a protein and another molecule. One of the approaches to assume protein functions from the genome sequences is to predict interactions between proteins and the molecules. Toward that goal, we have searched through interactions of proteins and other molecules in PDB to survey molecules of which interaction modes are available. In PDB, the molecules that interact with proteins are mainly small molecules except for DNA and RNA. Amongst about 16,000 entries in PDB, about 3,400 groups of small molecules are found to interact with proteins. Small molecules most often found in PDB are metal ions, such as magnesium, calcium and zinc. Sugar molecules are the next top small molecules found in PDB. Those molecules are known to act as cofactors for enzymes and/or stabilizers of the proteins. Understanding the interactions between those molecules and proteins is necessary to predict functions of proteins. The data is collected in the database and is freely available.
This work was supported by Grant-in-Aid for Scientific Research on Priority Areas (C) Genome Information Science from the Ministry of Education, Culture, Sports, Science and Technology of Japan and by grant for Research and Development for Applying Advanced Computational Science and Technology of Japan Science and Technology Corporation.
Category Intermolecular Interactions
