Lutz P. Ehrlich and Rebecca C. Wade
European Molecular Biology Laboratory, Meyerhofstr. 1, 69012 Heidelberg, Germany
Fax: +49 6221 387 517 Email: wade@embl-heidelberg.de
Introduction
In this review, we discuss current methods to predict the structure of a protein-protein complex,
given the structures of the respective proteins in their unbound conformations. We begin by putting
the protein-protein docking problem in context with respect to other biomolecular docking problems
and with respect to its role in the current genomic era. We then highlight the crucial points that
need to be considered when embarking on a docking project. We review the anatomy of prototypical
protein-protein interfaces and describe structural changes observed upon binding in experimentally
determined complexes. Then, after giving a brief overview of manual docking, we present automated
methods for docking. We describe current algorithms, their limitations, and the situations in which
they are applicable. After these descriptive review sections, we guide the reader through a case
study that illustrates some of the important points that should be considered in protein-protein
docking.
Rev. Comp. Chem. (2001) 17, 61-97.