PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB)

By Tamotsu Noguchi, H. Matsuda, Y. Akiyama. 2001

87 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Roland L. Dunbrack
2. Guoli Wang
3. Katsuhisa Horimoto
4. Akira R. Kinjo
5. Ken Nishikawa
6. Jinbo Xu
7. David Baker
8. Yang Zhang

In Molecular Biology

1. Guoli Wang
2. Roland L. Dunbrack
3. Katsuhisa Horimoto
4. Akira R. Kinjo
5. Ken Nishikawa
6. David Baker
7. Jinbo Xu
8. Yang Zhang

Citations in the corpus

• PISCES: a protein sequence culling server (2003, unknown): “The PDB-REPRDB server (Noguchi et al., 2001) provides a number of features, including an ability for the user to set parameters to generate customized lists.”
• PISCES: recent improvements to a PDB sequence culling server (2005, methodology): “In Table 1, we show the lengths of lists under various sequence identity cut-offs as determined by using BLAST, PSIBLAST and the REPRDB server (5), which use CLUSTALW and structure alignments.”
• PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003 (2003, unknown): “PDB-REPRDB (2,3) is a database of representative protein chains from the PDB, whose criteria used to select the representatives are: (a) quality of atomic coordinate data, (b) sequence uniqueness, and (c) conformation uniqueness that is particularly local.”
• Predicting absolute contact numbers of native protein structure from amino acid sequence (2004, methodology): “We first selected nonredundant protein chains with known 3D structures in the Protein Data Bank 20 (PDB) using PDB-REPRDB, 21 with conditions such as sequence identity less than 30%, sequence length (cid:5) 50, no membrane proteins, no nonstandard residues, no chain breaks, resolution better than 2…”