Creative BioMart provides protein-nucleic acid docking service to simulate the structure of protein and nucleic acid (DNA, RNA or hybrid DNA/RNA) complexes to determine protein-nucleic acid interaction and recognition, which is important for computer-aided drug design and complex structure prediction significance. With years of protein engineering research experience, we can provide you with the best quality and most professional services. If you are interested in our services, please do not hesitate to contact us for more information.

At the end of the 19th century, scientists used microscopes to observe the links between proteins and DNA strands and found that proteins interact with DNA and RNA, thereby affecting the structure and function of the corresponding nucleic acids. Protein-RNA and protein-DNA interactions form protein-nucleic acid complexes, which play roles in the regulation of transcription, translation, DNA replication, repair and recombination, RNA processing and translocation. These interactions are critical for cellular metabolism and the survival of all organisms. Furthermore, defects in protein-nucleic acid interactions are associated with many diseases, such as neurological disorders and cancer. With the development of computational docking methods, new structures of protein-nucleic acid complexes are solved and structural details of interactions are analyzed. Determining their complex structures has important implications for understanding biological processes at the atomic level and thus for their development.

Fig 1. The workflow of the NPDock server. (Tuszynska I, et al., 2015 )

Experimental determination of most protein-nucleic acid complex structures by high-resolution methods is a tedious and difficult process. Computational techniques can complement experimental approaches to elucidate protein-nucleic acid interactions. Creative BioMart utilizes various protein-nucleic acid docking web servers to accurately predict the structure of protein-nucleic acid complexes. A computational workflow is implemented including docking, pose scoring, clustering the top scoring models and optimizing the most promising solutions.

The workflow of protein-nucleic acid docking is as follows:

(1) Data input: It accepts data input for protein sequence and structure, of which currently only structure input for DNA/RNA is supported.

(2) Sequence similarity search: a sequence similarity search is performed against the PDB sequence database to find homologous sequences for receptor and ligand molecules.

(3) Structural modeling: models by comparing two sets of templates to see if they have common records of the same PDB code.

(4) Global docking: docking simulation through server modeling or user-uploaded structures.

Features of Protein-Nucleic Acid Docking

• Providing customers with a user-friendly web interface to enter the PDB structure and view the results.
• The docking process is fully automated and can help users save more than ten times the time required to run different methods separately.
• Not only structure but also sequence is accepted as protein input, and binding information from PDB can be automatically integrated.
• Intrinsic scoring functions that allow protein-protein and protein-DNA/RNA docking.
• Supporting modification of amino acid DNA/RNA molecules.
• Supporting docking of hybrid DNA-RNA molecules such as dsRNA/DNA duplexes.

Reference

1. Tuszynska I, Magnus M, Jonak K, et al.. (2015) NPDock: a web server for protein–nucleic acid docking[J]. Nucleic acids research. 43(W1): W425-W430.

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