Pairwise and multimeric protein-protein docking using the LZerD program suite

Methods Mol Biol. 2014;1137:209-34. doi: 10.1007/978-1-4939-0366-5_15.


Physical interactions between proteins are involved in many important cell functions and are key for understanding the mechanisms of biological processes. Protein-protein docking programs provide a means to computationally construct three-dimensional (3D) models of a protein complex structure from its component protein units. A protein docking program takes two or more individual 3D protein structures, which are either experimentally solved or computationally modeled, and outputs a series of probable complex structures.In this chapter we present the LZerD protein docking suite, which includes programs for pairwise docking, LZerD and PI-LZerD, and multiple protein docking, Multi-LZerD, developed by our group. PI-LZerD takes protein docking interface residues as additional input information. The methods use a combination of shape-based protein surface features as well as physics-based scoring terms to generate protein complex models. The programs are provided as stand-alone programs and can be downloaded from

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computational Biology / methods
  • Internet
  • Molecular Docking Simulation*
  • Multiprotein Complexes / chemistry*
  • Protein Binding
  • Protein Conformation*
  • Proteins / chemistry*
  • Software*


  • Multiprotein Complexes
  • Proteins