Docking Unbound Proteins with MIAX: A Novel Algorithm for Protein-Protein Soft Docking

Carlos A. Del Carpio Muñoz[1],[2] (
Tobias Peissker[3],[4] (
Atsushi Yoshimori[3] (
Eiichiro Ichiishi[1] (

[1]New Industry Creation Hatchery Center, Tohoku University, Aoba-ku, Sendai 980-8579, Japan
[2]Facultad de Farmaciay Bioquímica, Universidad Católica de Santa Moría, Umacollo s/n, Arequipa, Perú
[3]Laboratory for Bioinformatics, Department of Ecological Engineering, Toyohashi University of Technology, Tempaku, Toyohashi 441-8580, Japan
[4]Laboratory of Applied Physics, Dept. of Physics, Zwickau University of Applied Sciences, Dr. Friedrichsring 2A, Zwickau, Westsachsische, Germany


We propose a new methodology for “soft” docking unbound protein molecules (reported at the isolated state). The methodology is characterized by its simplicity and easiness of embedment in any rigid body docking process based on point complementarity. It is oriented to allow limited free but not unrealistic interpenetration of the side chains of protein surface amino acid residues. The central step to the technique is a filtering process similar to those in image processing. The methodology assists in deletion of atomic-scale details on the surface of the interacting monomers, leading to the extraction of the most characteristic flattened shape for the molecule as well as the definition of a soft layer of atoms to allow smooth interpenetration of the interacting molecules during the docking process. Although the methodology does not perform structural or conformational rearrangements in the interacting monomers, results output by the algorithm are in fair agreement with the relative position of the monomer in experimentally reported complexes. The algorithm performs especially well in cases where the complexity of the protein surfaces is high, that is in hetero dimmer complex prediction. The algorithm is oriented to play the role of a fast screening engine for proteins known to interact but for which no information other than that of the structures at the isolated state is available. Consequently the importance of the methodology will increase in structural-function studies of thousand of proteins derived from large scale genome sequencing projects being executed all around the globe.

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Japanese Society for Bioinformatics