The resource NPIDB (Nucleic acid – Protein Interaction DataBase) includes a collection of files in the PDB format containing structural information on DNA-protein and RNA-protein complexes, and a number of online tools for analysis of the complexes. The tools are: an original program CluD for analysis of hydrophobic clusters on interfaces, program for detecting potential hydrogen bonds and water bridges, visualization of structures with Jmol. Information on SCOP and Pfam domains detected in protein chains is presented.
Reference: Kirsanov et al. NPIDB: nucleic acid–protein interaction database. Nucleic Acid Research, Volume 41 Issue D1 D517-D523 (January 2013)

   Structures of protein-nucleic acid complexes are extracted from Protein Data Bank (PDB) as files in the PDB format.

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  As of 23.09.2015 there are 5547 structures.

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   Each individual complex has its own web page, containing general information, links to other resources (e.g., PDBsum and BIPA), a table describing biological units or models, tables describing Pfam and SCOP domains in protein chains, and the list of available actions (including Jmol visualization)

  The detection of Pfam domains is done using the HMM profiles downloaded from Pfam server. Each family has its own web page with the list of entries that include domains of the family. Best resolution representatives of Pfam families are available for download or viewing with Jmol.

   List of SCOP domains occurred in DNA-protein and RNA-protein complexes is organized in tree-like form, according to the SCOP classification. For each SCOP family a web-page is created. It contains the list of entries that include domains of the family.

  For most SCOP families of DNA-recognizing domains a structural alignment of the family is stored together with an accompanying information. These families are classified according to their modes of DNA-protein interaction, which means the contacting part of DNA (e.g., the major groove) and the contacting elements of protein secondary structure (e.g., alpha-helices).

Belozersky Institute of Moscow State University: http://www.belozersky.msu.ru
Department of Mathematical Methods in Biology, team "Sequences&structures": http://mouse.genebee.msu.ru/
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