ABSTRACT
This chapter explains prediction of three-dimensional structure of protein-biomolecule complexes; concepts, the docking problem and practical considerations. It discusses molecular complementarity; using shape, surface properties, molecular mechanics and knowledge-based force fields and experimental constraints. Displaying physical properties on the molecular surface of molecules can help to guide molecular docking. Alternatively sequence conservation might also help, particularly where a homologous family of proteins maintain a specific binding partner. The electrostatic properties of biomolecules often play an important role in determining interactions. Determining the structure of two interacting proteins still remains a formidable problem. The problem is a six dimensional search problem with three degrees of translational freedom and three degrees of rotational freedom for the mobile molecule assuming one molecule is kept stationary. Visualization methods are very important in viewing molecular properties on molecules. The popular program RasMol can be made to view molecular properties by assigning the properties to the temperature factor column of the PDB file in question.
