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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.
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.
A database containing sets of in vitro selected transcription factor (TF) binding site sequences obtained with systematic evolution of ligands by exponential enrichment (SELEX) method. HTPSELEX offers reasonably large SELEX libraries obtained with conventional low-throughput protocols. Development of HTPSELEX is motivated by computer simulations showing that several thousands of individual sequences are required to derive an accurate description of the sequence specificity of a typical TF.
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.
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.
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.
dbAMEPNI / database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions
Delivers a collection of alanine mutagenic data for protein-nucleic acid interfaces. dbAMEPNI contains alanine mutagenic effects for over 850 mutations in more than 200 protein-nucleic acid complexes. It is composed of structural data such as: solvent accessible surface areas (SASA), secondary structure and hydrogen bonds. This database assists in the investigation of protein-nucleic acid interactions.
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.
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