HDOCK update for modeling protein‐RNA/DNA complex structures

Abstract

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.

Novel enzyme-linked aptamer-antibody sandwich assay and hybrid lateral flow strip for SARS-CoV-2 detection

“…The procedure of amplification variable-region genes of monoclonal antibody was outlined in supplementary section (Amplification variable-region genes of monoclonal antibody). The secondary structures of mAb-6F6E11 and selected ssDNA aptamers were predicted using the SWISS-MODEL web server ( https://swissmodel.expasy.org/ ) [ 20 , 21 ] and RNAfold web server ( http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi ) [ 22 ], respectively, while the docking sites of the mAb-6F6E11 or aptamers to the SARS-CoV-2 N protein were predicted using the HDOCK web server ( http://hdock.phys.hust.edu.cn ) [ 23 ].…”

Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation

“…Moreover, other specialized docking tools are available for protein–RNA/DNA complexes. These include NPDock, a computational workflow that combines the GRAMM program with a statistical potential for scoring protein–RNA/DNA complexes, and HDOCK, a web server − that accepts RNA and protein structures, along with protein sequences, as input. If the protein structure is unknown, HDOCK performs a sequence similarity search against the Protein Data Bank to identify the homologous proteins.…”

Structure–Function Analysis of RBP7910: An Editosome Z-Binding Protein in Trypanosomatids

“…Doublestranded (ds) non-Z-RNA oligonucleotides were generated by uploading the raw sequence into the HDOCK RNA/DNA 3D structure modeling tool, which for ds RNA/DNA inputs constructs a 3D structure using X3DNA, an integrated tool in HDOCK (http://hdock.phys. hust.edu.cn/ accessed on 12 September 2023), and a 5000-step AMBER59 MD minimization refinement [23]. Z-form oligonucleotides (d(GC)6, r(GC)6, and r(UA)6) were copied from a ds DNA GC-repeat oligonucleotide featuring a BZ junction (PDB ID: 5zuo), edited manually in DSV to include relevant non-binding site nucleotides towards the ligand 3 end.…”