Improved side-chain modeling for protein-protein docking

Chu Wang, Ora Schueler-Furman, David Baker*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

198 Scopus citations


Success in high-resolution protein-protein docking requires accurate modeling of side-chain conformations at the interface. Most current methods either leave side chains fixed in the conformations observed in the unbound protein structures or allow the side chains to sample a set of discrete rotamer conformations. Here we describe a rapid and efficient method for sampling off-rotamer side-chain conformations by torsion space minimization during protein-protein docking starting from discrete rotamer libraries supplemented with side-chain conformations taken from the unbound structures, and show that the new method improves side-chain modeling and increases the energetic discrimination between good and bad models. Analysis of the distribution of side-chain interaction energies within and between the two protein partners shows that the new method leads to more native-like distributions of interaction energies and that the neglect of side-chain entropy produces a small but measurable increase in the number of residues whose interaction energy cannot compensate for the entropie cost of side-chain freezing at the interface. The power of the method is highlighted by a number of predictions of unprecedented accuracy in the recent CAPRI (Critical Assessment of PRedicted Interactions) blind test of protein-protein docking methods.

Original languageAmerican English
Pages (from-to)1328-1339
Number of pages12
JournalProtein Science
Issue number5
StatePublished - May 2005
Externally publishedYes


  • Protein-protein docking
  • Rotamer minimization
  • Side-chain entropy
  • Side-chain modeling


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