Skip to main content

Software for molecular docking: a review


Molecular docking methodology explores the behavior of small molecules in the binding site of a target protein. As more protein structures are determined experimentally using X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy, molecular docking is increasingly used as a tool in drug discovery. Docking against homology-modeled targets also becomes possible for proteins whose structures are not known. With the docking strategies, the druggability of the compounds and their specificity against a particular target can be calculated for further lead optimization processes. Molecular docking programs perform a search algorithm in which the conformation of the ligand is evaluated recursively until the convergence to the minimum energy is reached. Finally, an affinity scoring function, ΔG [U total in kcal/mol], is employed to rank the candidate poses as the sum of the electrostatic and van der Waals energies. The driving forces for these specific interactions in biological systems aim toward complementarities between the shape and electrostatics of the binding site surfaces and the ligand or substrate.

This is a preview of subscription content, access via your institution.


Download references

Author information

Authors and Affiliations


Corresponding author

Correspondence to Nataraj S. Pagadala.

Ethics declarations

Conflict of interest

Nataraj S. Pagadala declares that he has no conflict of interest. Khajamohiddin Syed declares that he has no conflict of interest. Jack Tuszynski declares that he has no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Pagadala, N.S., Syed, K. & Tuszynski, J. Software for molecular docking: a review. Biophys Rev 9, 91–102 (2017).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:


  • Rigid body docking
  • Flexible docking
  • Docking accuracy