| abstract |
The instant invention provides methods and computational tools for designing interaction between molecules based on their three-dimensional atomic coordinates. In a preferred embodiment, the method can be used to design protein-protein interactions based on their three-dimensional structure. In one embodiment, the method of the instant invention includes a first step of docking interacting molecules based on their surface geometric fit by quantitative correlation techniques, followed by a second step of optimizing the resulting interacting surface by altering interface side-chains, such that the interfacial side-chains are repacked in a manner analogous to the cores of well-folded proteins. The method can be used in numerous applications, including redesigning interaction interfaces between known protein-protein, protein-polynucleotide, protein-carbohydrates (such as polysaccharide), protein-lipid (or steroid), enzyme-inhibitor, or antibody-target epitope pairs, or rational design of more potent drug molecules. |