The phenotype of every known living organism is determined mainly by the compli- cated interactions between the proteins produced in this organism. Understanding the orchestration of the organismal responses to the external or internal stimuli is based on the understanding of the interactions of individual proteins and their complexes structures. The prediction of a complex of two or more proteins is the problem of the protein-protein docking field. Docking algorithms usually have two major steps: exhaustive 6D rigid-body search followed by the scoring. In this work we made contribution to both of these steps. We developed a novel algorithm for 6D exhaustive search, HermiteFit. It is based on Hermite decomposition of 3D functions into the Hermite basis. We implemented this algorithm in the program for fit- ting low-resolution electron density maps. We showed that it outperforms existing algorithms in terms of time-per-point while maintaining the same output model accuracy. We also developed a novel approach to computation of a scoring function, which is based on simple logical arguments and avoids an ambiguous com- putation of the reference state. We compared it to the existing scoring functions on the widely used protein-protein docking benchmarks. Finally, we developed an approach to include water-protein interactions into the scoring functions and val- idated our method during the Critical Assessement of Protein Interactions round 47.