How to do DNA-Protein site specific docking?

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Pranabesh Mandal

HDOCK can be used to perform DNA-Protein docking.

The web server can be accessed at:

http://hdock.phys.hust.edu.cn/

Susanta Roy

There are several tools and servers available for DNA-protein site-specific docking, including:

HADDOCK (High Ambiguity Driven biomolecular DOCKing): This is a widely used software for docking macromolecules, including proteins, nucleic acids, and their complexes. HADDOCK is capable of performing site-specific docking by specifying the active site residues of both the protein and the DNA molecule. HADDOCK can be downloaded and run locally or accessed through a web server.

PatchDock: This is a user-friendly docking server that performs protein-DNA docking. It allows the user to specify the active site residues of both the protein and DNA molecule. The server generates several possible docking solutions and ranks them based on their predicted binding energies.

HEX (High-speed EXhaustive docking): This is another widely used software for docking macromolecules, including proteins and nucleic acids. HEX is capable of performing site-specific docking by specifying the active site residues of both the protein and DNA molecule. It can be downloaded and run locally.

ClusPro: This is a fully automated docking server that can perform docking between proteins and nucleic acids. ClusPro is capable of performing site-specific docking by specifying the active site residues of both the protein and DNA molecule. The server generates several possible docking solutions and ranks them based on their predicted binding energies.