We are analyzing https://link.springer.com/article/10.1186/1471-2105-11-262.

Title:
The Protein-DNA Interface database | BMC Bioinformatics
Description:
The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 Å or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface. We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes.
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28 years and 1 months (reg. 1997-05-29).

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Keywords {🔍}

dna, protein, interface, database, pubmed, proteindna, article, interactions, figure, pdb, google, scholar, interfaces, cas, complexes, features, structure, interaction, atoms, effective, information, panel, complex, proteins, search, binding, defined, data, classification, detailed, structures, atomic, interacting, file, atom, number, web, central, types, recognition, user, entry, software, table, section, original, independent, bases, groove, authors,

Topics {✒️}

protein data bank open-source java viewer semi-automated filtered search protein-nucleic acid interaction protein-nucleic acid complexes main types helix-turn-helix protein-dna binding specificity structural/dna binding protein passive base-flipping mechanism sequence-directed dna loading article download pdf resemble canonical h-bond protein-nucleic acid interactions classifying protein-dna complexes regulatory protein dna-complexes effective knowledge-based potentials protein-dna recognition process article norambuena protein-nucleic acid interfaces independent clustering/grouping schemes water-mediated hydrogen bonds site-specific recombination synapse nucleic acids-protein interactions left-handed dna conformation green-highlighted atoms belong blue-highlighted atoms belong protein-dna complexes solved solved protein-dna complexes independent protein-dna interface protein-dna complexes based protein-dna atom pairs full size image independent protein-dna interfaces complete biological unit simple function/structure-based classification privacy choices/manage cookies authors’ original file single protein-dna interface protein-dna interface database protein-dna interactions resources detailed data calculated class transcription factor transcription factor class biomed central distinct binding specificity protein-protein interaction canonical hydrogen bonds chemical/structural/groove position gene expression red balls represent

Schema {🗺️}

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         Algorithms
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