SMD: Visual Steering of Molecular Dynamics for Protein Design

Computers have become an essential component of molecular modeling work, especially for complex biomolecules. They are commonly used for such tasks as modeling the docking between ligand and receptor molecules, structure refinement from X-ray crystallography and NMR data, and sequence analysis. Newer tools are intended to aid in designing new proteins as well as analyzing those found in nature. Designing proteins not found in nature is a rapidly developing field. In part, such designs serve to test the validity and applicability of computational molecular models. As experience with de novo design grows, proteins may be tailored for specific effects, such as new types of drugs.