Protein-nucleic acid interactions are involved in various cellular processes. Therefore, determining the structures of protein-nucleic acid complexes can provide insights into the mechanisms of the interactions and thus guide the rational drug design to modulate these interactions. Due to the high cost and technical difficulties of solving complex structures experimentally, computational modeling such as molecular docking has been playing an important role in the study of molecular interactions. In order to make it easier for researchers to obtain biomolecular complex structures through molecular docking, we developed the HDOCK server for protein-protein and protein-RNA/DNA docking (accessed at http://hdock.phys.hust.edu.cn/). Since its first release in 2017, HDOCK has been widely used in the scientific community. As nucleic acids may include single-stranded (ss) RNA/DNA and double-stranded (ds) RNA/DNA, we now present an updated version of HDOCK, which offers new options for structural modeling of ssRNA, ssDNA, dsRNA, and dsDNA. We hope this update will better help the scientific community solve important biological problems, thereby advancing the field. In this article, we describe the general protocol of HDOCK with emphasis on the new functions on RNA/DNA modeling. Several application examples are also given to illustrate the usage of the new functions.
Keywords: double-stranded RNA/DNA; molecular docking; protein-RNA/DNA interactions; scoring function; single-stranded RNA/DNA.
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