Docking unbound proteins using shape complementarity, desolvation, and electrostatics

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Abstract
A comprehensive docking study was performed on 27 distinct protein‐protein complexes. For 13 test systems, docking was performed with the unbound X‐ray structures of both the receptor and the ligand. For the remaining systems, the unbound X‐ray structure of only molecule was available; therefore the bound structure for the other molecule was used. Our method optimizes desolvation, shape complementarity, and electrostatics using a Fast Fourier Transform algorithm. A global search in the rotational and translational space without any knowledge of the binding sites was performed for all proteins except nine antibodies recognizing antigens. For these antibodies, we docked their well‐characterized binding site—the complementarity‐determining region defined without information of the antigen—to the entire surface of the antigen. For 24 systems, we were able to find near‐native ligand orientations (interface Cα root mean square deviation less than 2.5 Å from the crystal complex) among the top 2,000 choices. For three systems, our algorithm could identify the correct complex structure unambiguously. For 13 other complexes, we either ranked a near‐native structure in the top 20 or obtained 20 or more near‐native structures in the top 2,000 or both. The key feature of our algorithm is the use of target functions that are highly tolerant to conformational changes upon binding. If combined with a post‐processing method, our algorithm may provide a general solution to the unbound docking problem. Our program, called ZDOCK, is freely available to academic users (http://zlab.bu.edu/∼rong/dock/). Proteins 2002;47:281–294.