In other words, the program exploits the inherent degrees of freedom present in a chain of amino acid residues - two angles of rotation per residue - to move substructures without violating local chemical invariants such as bond distances or bond angles. The program uses an inverse kinematics approach to translate the user's dragging motions into dihedral angle changes along amorphous coil regions connecting a selected substructure to the rest of the protein. It uses a direct manipulation interface, allowing users to select arbitrary substructures (alpha-helices, beta-strands) of a protein and drag them to create tertiary structures such as sheets of aligned beta-strands or clusters of alpha-helices. ProtoShop is an interactive visualization program for 3D protein structures, but it focuses on interactive modelling methods to create reasonable initial configurations for global energy optimization.

These structures are then used as initial configurations for an optimization algorithm. Our work focuses on providing an interactive, visual tool assisting a user to rapidly create many three-dimensional protein structures for a given amino acid sequence. When using human intuition and biological knowledge to create initial configurations it is highly likely that much better predictions can be obtained in much less computing time. Since the optimization problem is high-dimensional and the energy function contains local extrema in abundance, it is important to provide an optimization program with a diverse set of chemically and biologically reasonable initial configurations. It is commonly believed that the native shape of a protein is the one corresponding to the global minimum of its internal energy and the protein folding problem has been treated as an optimization problem in recent years, to some success. A protein's primary structure, i.e., its amino acid sequence, is directly encoded in its DNA sequence this, however, is a purely one-dimensional structure that does not directly encode a three-dimensional shape. One of the grand challenges in computational biology is the prediction of the three-dimensional structure of a protein from its chemical makeup alone.

Download primary structure of protein