Low-resolution docking: Prediction of complexes for underdetermined structures

One of the most fundamental questions concerning ligand-receptor interaction is whether such a process of intermolecular association is generally determined by local structural elements of the participating molecules, or whether there are also large-scale motifs in molecule structures that facilitate complex formation. From the point of view of practical docking computations, the elaborate character of local structural details in ligand-receptor interaction creates a large number of false-positive matches, which interfere with determination of the best fit. Another significant obstacle in protein docking is the problem of structural data inaccuracy (poor structure resolution, conformational changes upon complex formation, etc.). Our study Vakser (1995) Protein Eng., 8, 371-377, based on ultralow (approximately 7 A resolution) representation of molecular structures, allowes to average all high-resolution structural details, and still predict most of the structural features of the ligand-receptor complex. The approach dramatically improves the signal-to-noise ratio in determination of the best fit, and moves the structure inaccuracy tolerance to the range of the macrostructure. In the present paper, we describe a further validation of the main principles of this approach and a detailed analysis of the low-resolution docking results. This includes clustering of ligand positions around the receptor molecule and cross-validation of ligands and receptors from different complexes. We also discuss the important implications of the approach to the multiple-minima problem and a possible role of different structural elements in the recognition mechanism.