About Databases of PRF

■Protein Data Bank (PDB)

Contents of information:

Protein Data Bank is the single global archive of experimentally determined macromolecular structures. The PRF is collaborating with Protein Data Bank Japan (PDBj) of the Institute for Protein Research, Osaka University, and operating the branch office of PDBj where the deposited entries are locally processed. This activity is financially supported by JST NBDC (JPMJND2205).

■Literature Database (PRF/LITDB)

Scope of collection of literature:

We select all articles dealing with peptides from scientific journals accessible in Japan. "Peptides" here were mainly of 50 amino acids or fewer residues, but those of 50 to 100 amino acid residues have been included in Volume 14 in the year of 1988 and thereafter. Articles dealing with structural aspects of proteins and chemical aspects of receptors and processing enzymes of peptide hormones are cited regardless of the number of amino acid residues. Moreover, articles about antigenic sites, functional sites and active fragments of proteins are cited.

Contents of information:

For each article cited, an abstract of the contents composed by specialists is given in addition to bibliographic items such as journal names, author names and titles. For convenience of retrieval, selected articles are classified into the following categories:

A, News, Reviews and Comments
B, Theoretical, Physicochemical and Inorganic
C, Organic and Synthetic
D, Biochemical and Analytical
E, Biological, Physiological and Medical
G, Others

■Peptide/Protein Sequence Database (PRF/SEQDB)

Contents of information:

This database consists of amino acid sequrences of peptides and proteins, including sequences predicted from genes. You can also search literature in which the sequence is presented. Sequences not included in EMBL, GenBank and SwissProt are also found in PRF/SEQDB since it is constructed on the basis of all amino acid sequences of peptides and proteins reported in literature.

■Synthetic Compounds Database (PRF/SYNDB)

Contents of information:

Unnatural amino acids, amino acid derivatives and chemically synthesized peptides are registered. Intermediates are also collected. You can search literature about chemical synthesis by compound names or components.

■Number of entries of databases:

LITDB: 847,700 entries
SEQDB: 1,392,774 entries
SYNDB: 297,801 entries
PEPDB: 11,456 entries

as of 2024-04-08.


		About Databases of PRF ■Protein Data Bank (PDB) Contents of information: Protein Data Bank is the single global archive of experimentally determined macromolecular structures. The PRF is collaborating with Protein Data Bank Japan (PDBj) of the Institute for Protein Research, Osaka University, and operating the branch office of PDBj where the deposited entries are locally processed. This activity is financially supported by JST NBDC (JPMJND2205). ■Literature Database (PRF/LITDB) Scope of collection of literature: We select all articles dealing with peptides from scientific journals accessible in Japan. "Peptides" here were mainly of 50 amino acids or fewer residues, but those of 50 to 100 amino acid residues have been included in Volume 14 in the year of 1988 and thereafter. Articles dealing with structural aspects of proteins and chemical aspects of receptors and processing enzymes of peptide hormones are cited regardless of the number of amino acid residues. Moreover, articles about antigenic sites, functional sites and active fragments of proteins are cited. Contents of information: For each article cited, an abstract of the contents composed by specialists is given in addition to bibliographic items such as journal names, author names and titles. For convenience of retrieval, selected articles are classified into the following categories: A, News, Reviews and Comments B, Theoretical, Physicochemical and Inorganic C, Organic and Synthetic D, Biochemical and Analytical E, Biological, Physiological and Medical G, Others ■Peptide/Protein Sequence Database (PRF/SEQDB) Contents of information: This database consists of amino acid sequrences of peptides and proteins, including sequences predicted from genes. You can also search literature in which the sequence is presented. Sequences not included in EMBL, GenBank and SwissProt are also found in PRF/SEQDB since it is constructed on the basis of all amino acid sequences of peptides and proteins reported in literature. ■Synthetic Compounds Database (PRF/SYNDB) Contents of information: Unnatural amino acids, amino acid derivatives and chemically synthesized peptides are registered. Intermediates are also collected. You can search literature about chemical synthesis by compound names or components. ■Number of entries of databases: LITDB: 847,700 entries SEQDB: 1,392,774 entries SYNDB: 297,801 entries PEPDB: 11,456 entries as of 2024-04-08.