DNAproDB: an updated database for the automated and interactive analysis of protein-DNA complexes

Raktim Mitra; Ari S Cohen; Jared M Sagendorf; Helen M Berman; Remo Rohs

doi:10.1093/nar/gkae970

DNAproDB: an updated database for the automated and interactive analysis of protein-DNA complexes

Nucleic Acids Res. 2024 Nov 4:gkae970. doi: 10.1093/nar/gkae970. Online ahead of print.

Authors

Raktim Mitra¹, Ari S Cohen¹, Jared M Sagendorf¹, Helen M Berman^{1

2}, Remo Rohs^{1

3

4

5}

Affiliations

¹ Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
² Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA.
³ Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.
⁴ Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
⁵ Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA.

PMID: 39494533
DOI: 10.1093/nar/gkae970

Abstract

DNAproDB (https://dnaprodb.usc.edu/) is a database, visualization tool, and processing pipeline for analyzing structural features of protein-DNA interactions. Here, we present a substantially updated version of the database through additional structural annotations, search, and user interface functionalities. The update expands the number of pre-analyzed protein-DNA structures, which are automatically updated weekly. The analysis pipeline identifies water-mediated hydrogen bonds that are incorporated into the visualizations of protein-DNA complexes. Tertiary structure-aware nucleotide layouts are now available. New file formats and external database annotations are supported. The website has been redesigned, and interacting with graphs and data is more intuitive. We also present a statistical analysis on the updated collection of structures revealing salient patterns in protein-DNA interactions.

Abstract

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