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Wiley, Protein Science, 5(14), p. 1328-1339

DOI: 10.1110/ps.041222905

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Improved side-chain modeling for protein–protein docking

Journal article published in 2005 by Chu Wang, Ora Schueler-Furman ORCID, David Baker
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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 entropic 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.