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. 2016 Dec 1:6:38144.
doi: 10.1038/srep38144.

G4IPDB: A database for G-quadruplex structure forming nucleic acid interacting proteins

Subodh Kumar Mishra  1 , Arpita Tawani  1 , Amit Mishra  2 , Amit Kumar  1
Affiliations

G4IPDB: A database for G-quadruplex structure forming nucleic acid interacting proteins

Subodh Kumar Mishra et al. Sci Rep. .

Abstract

Nucleic acid G-quadruplex structure (G4) Interacting Proteins DataBase (G4IPDB) is an important database that contains detailed information about proteins interacting with nucleic acids that forms G-quadruplex structures. G4IPDB is the first database that provides comprehensive information about this interaction at a single platform. This database contains more than 200 entries with details of interaction such as interacting protein name and their synonyms, their UniProt-ID, source organism, target name and its sequences, ∆Tm, binding/dissociation constants, protein gene name, protein FASTA sequence, interacting residue in protein, related PDB entries, interaction ID, graphical view, PMID, author's name and techniques that were used to detect their interactions. G4IPDB also provides an efficient web-based "G-quadruplex predictor tool" that searches putative G-quadruplex forming sequences simultaneously in both sense and anti-sense strands of the query nucleotide sequence and provides the predicted G score. Studying the interaction between proteins and nucleic acids forming G-quadruplex structures could be of therapeutic significance for various diseases including cancer and neurological disease, therefore, having detail information about their interactions on a single platform would be helpful for the discovery and development of novel therapeutics. G4IPDB can be routinely updated (twice in year) and freely available on http://bsbe.iiti.ac.in/bsbe/ipdb/index.php.

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Figures

Figure 1
Figure 1. Home Page of G4IPDB.
Depicting the browse, search, G4-predictor tool and contact options.
Figure 2
Figure 2. Schematic representation of the architecture of G4IPDB.
Figure 3
Figure 3. Browse and Search Options.
Screenshots of (a) Browse option showing classified organization of G4IPDB and (b) Search options showing different searching criteria.
Figure 4
Figure 4. G-quadruplex DNA/RNA interacting proteins.
Screenshots showing results of browsing (a) G-quadruplex DNA interacting protein and (b) G-quadruplex RNA interacting protein.
Figure 5
Figure 5. Various option available in Interaction ID.
Screenshot showing various options of information about target nucleic acid and interacting proteins while browsing any Interaction ID present in the G4IPDB.
Figure 6
Figure 6. G4 predictor tool.
Screenshots showing search methods in the G4 predictor tool.
Figure 7
Figure 7. Results of G4 predictor tool.
Screenshots of results showing various predicted putative G-quadruplex motif in the queried nucleotide sequences.
Figure 8
Figure 8. Schematic representation for the various applications of G4IPDB.
See this image and copyright information in PMC

References

    1. Endoh T. & Sugimoto N. Mechanical insights into ribosomal progression overcoming RNA G-quadruplex from periodical translation suppression in cells. Sci. Rep. 6, 22719 (2016). - PMC - PubMed
    1. Lane A. N., Chaires J. B., Gray R. D. & Trent J. O. Stability and kinetics of G-quadruplex structures. Nucleic Acids Res. 36, 5482–5515 (2008). - PMC - PubMed
    1. Keniry M. A. Quadruplex structures in nucleic acids. Biopolymers 56, 123–46 (2000). - PubMed
    1. Kogut M., Kleist C. & Czub J. Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad-a common structural unit of G-quadruplex DNA. Nucleic Acids Res. 44, 3020–30 (2016). - PMC - PubMed
    1. Bochman M. L., Paeschke K. & Zakian V. A. DNA secondary structures: stability and function of G-quadruplex structures. Nat. Rev. Genet. 13, 770–780 (2012). - PMC - PubMed