PyDockDNA: A new web server for energy-based protein-DNA docking and scoring.

ABSTRACT: Proteins and nucleic acids are essential biological macromolecules for cell life. Indeed, interactions between proteins and DNA regulate many biological processes such as protein synthesis, signal transduction, DNA storage, or DNA replication and repair. Despite their importance, less than 4% of total structures deposited in the Protein Data Bank (PDB) correspond to protein-DNA complexes, and very few computational methods are available to model their structure. We present here the pyDockDNA web server, which can successfully model a protein-DNA complex with a reasonable predictive success rate (as benchmarked on a standard dataset of protein-DNA complex structures, where DNA is in B-DNA conformation). The server implements the pyDockDNA program, as a module of pyDock suite, thus including

SUBMITTER: Rodriguez-Lumbreras LA 

PROVIDER: S-EPMC9582769 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature