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NPIDB / Nucleic Acids—Protein Interaction DataBase

Provides an access to information about all available structures of DNA–protein and RNA–protein complexes. The NPIDB database contains comparative structural information on some SCOP families. It also includes a collection of files in PDB format containing structural information on DNA–protein and RNA–protein complexes extracted from PDB, and a number of online tools for analysis of the complexes. All structural files of NPIDB are downloadable.


Catalogues demonstrated sites and non-sites for Escherichia coli DNA-binding proteins. DPInteract is a collection of search matrices from alignments of available experimental proteins. This dataset is being collected with several purposes: (i) Aids the annotation of such sites in other E. coli databases and sequence entries, (ii) interprets the results of whole-genome in vivo methylation protection experiments and (iii) develops better computational tools for recognizing DNA binding proteins in sequence data.


Performs structure analysis of DNA–protein complexes and extract structural features from the complex via an automated structure-processing pipeline. DNAproDB provides a database of DNA–protein complexes and a unique, interactive visualizations for each structure, which can be exported and downloaded at high resolution. Users can process a structure using the DNAproDB pipeline and can visualize extracted features from a generated report page for the structure by uploading a structure file of a DNA–protein complex.


Contains information about the MYC, a gene that has several functions: in cell growth, differentiation, apoptosis, or genomic stability. MYCbase is a tertiary database compiling various aspects of Myc relevant to cancer biology. The information presented in the website can be classified in the following categories: mutation, protein-protein interaction (PPI), gene expression, PRIDE, protein-protein interaction modulators, miRNA interaction, pathway/metabolism, methylation, protein abundance, DNA interaction, post-translational modifications (PTMs). This tool represents a database on which the users can download the information freely.

PDSA / Protein-DNA Structure-Affinity Database

Contains protein-DNA structural complexes. PDSA is suitable for general use in the analysis of the relationship between sequence and structure. It can assist users to retrieve helix-turn-helix (HTH)-DNA complexes using all available fields on the web site, including gene and protein names, motif types, and source organism. The data contained is PDSA have been processed to standardize their chain ordering and connectivity, and to remove any pathologies.

BIPA / Biological Interaction database for Protein-nucleic Acid

Stores protein-nucleic acid interaction. BIPA is a database that provides various features of protein–nucleic acid interfaces and non-redundant multiple structural alignments for nucleic acid-binding families. The database allows analyze on the patterns and the impact of mutations on the protein-nucleic acid interfaces. User can search nucleic acid-binding proteins and their interfaces and also identify interfaces of similar shape in different protein families.