Protein tertiary structure prediction using a branch and bound algorithm

We report a new method for predicting protein tertiary structure from sequence and secondary structure information. The predictions result from global optimization of a potential energy function, including van der Waals, hydrophobic, and excluded volume terms. The optimization algorithm, which is based on the αBB method developed by Floudas and coworkers (Costas and Floudas, J Chem Phys 1994;100:1247–1261), uses a reduced model of the protein and is implemented in both distance and dihedral angle space, enabling a side‐by‐side comparison of methodologies. For a set of eight small proteins, representing the three basic types—all α, all β, and mixed α/β—the algorithm locates low‐energy native‐like structures (less than 6Å root mean square deviation from the native coordinates) starting from an unfolded state. Serial and parallel implementations of this methodology are discussed. Proteins 1999;35:41–57. © 1999 Wiley‐Liss, Inc.