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  • Title: Protein tertiary structure prediction using a branch and bound algorithm.
    Author: Eyrich VA, Standley DM, Felts AK, Friesner RA.
    Journal: Proteins; 1999 Apr 01; 35(1):41-57. PubMed ID: 10090285.
    Abstract:
    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 alphaBB 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 alpha, all beta, and mixed alpha/beta--the algorithm locates low-energy native-like structures (less than 6A root mean square deviation from the native coordinates) starting from an unfolded state. Serial and parallel implementations of this methodology are discussed.
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