Protein tertiary structure prediction using a branch and bound algorithm.

V A Eyrich; D M Standley; A K Felts; R A Friesner

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PubMed · 10090285

Protein tertiary structure prediction using a branch and bound algorithm.

V A Eyrich·D M Standley·A K Felts·R A Friesner

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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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Algorithms Computer Simulation Models, Chemical Monte Carlo Method Protein Folding Protein Structure, Tertiary Journal Article Research Support, U.S. Gov't, P.H.S.

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V A Eyrich, D M Standley, A K Felts, R A Friesner. 1999-04-01. Protein tertiary structure prediction using a branch and bound algorithm.. https://pubmed.ncbi.nlm.nih.gov/10090285/

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