Ab Initio Calculation of Protein Structure by
Global Optimization of Potential Energy

Professor Harold Scheraga
March 6, 2002

Professor Harold Scheraga has suggested the following background reading:

1. J. Pillardy, Y.A. Arnautova, C. Czaplewski, K.D. Gibson, and H.A. Scheraga† Conformation-family Monte Carlo: A new method for crystal structure prediction, Proc. Natl. Acad. Sci., U.S.A., 98, 12351-12356 (2001).

2. J. Pillardy, C. Czaplewski, A. Liwo, W.J. Wedemeyer, J. Lee, D.R. Ripoll, P. Arlukowicz, S. Oldziej, Y.A. Arnautova and H.A.Scheraga† Development of physics-based energy functions thatvpredict medium-resolution structures for protein of the Š, ‚ and Š/‚ structural classes, J. Phys. Chem. B, 105, 7299-7311 (2001).

3. J. Lee, D.R. Ripoll, C. Czaplewski, J. Pillardy, W.J. Wedemeyer and H.A. Scheraga† Optimization of parameters in macromolecular potential energy functions by conformational space annealing, J. Phys. Chem. B., 105, 7291-7298 (2001).

4. A. Liwo, C. Czaplewski, J. Pillardy and H. A. Scheraga†Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field, J. Chem. Phys., 115, 2323-2347 (2001).

5. J. Pillardy, C. Czaplewski, A. Liwo, J. Lee, D.R. Ripoll, R. Kazmierkiewicz, S. Oldziej, W. J. Wedemeyer, K.D. Gibson, Y.A. Arnautova, J. Saunders, Y.-J. Ye and H.A. Scheraga† Recent improvements in prediction of protein structure by global optimization of a potential energy function, Proc. Natl. Acad. Sci., U.S.A., 98, 2329-2333 (2001).

6 J. Pillardy, C. Czaplewski, W.J. Wedemeyer and H.A. Scheraga† Conformation-Family Monte Carlo (CFMC): An efficient computational method for identifying the low-energy states of a macromolecule, Helv. Chim. Acta, 83, 2214-2230 (2000).

7 J. Lee, J. Pillardy, C. Czaplewski, Y. Arnautova, D.R. Ripoll, A. Liwo, K.D. Gibson, R.J. Wawak, and H.A. Scheraga† Efficient parallel algorithms in global optimization of potential energy functions, Comput. Physics Commun., 128, 399-411 (2000).

8 J. Lee, A. Liwo, D.R. Ripoll, J. Pillardy, J.A. Saunders, K.D. Gibson and H.A. Scheraga Hierarchical energy-based approach to protein-structure prediction: Blind-test evaluation with CASP3 targets, Intl. J. Quantum Chem., 71, 90-117 (2000).

9 J. Pillardy, R.J. Wawak, Y.A. Arnautova, C. Czaplewski, and H.A. Scheraga† Crystal structure prediction by global optimization as a tool for evaluating potentials: Role of the dipole moment correction term in successful predictions, J. Am. Chem. Soc., 122, 907-921 (2000).

10 H.A. Scheraga, J. Lee, J. Pillardy, Y.-J. Ye, A. Liwo, and D.R. Ripoll Surmounting the multiple-minima problem in protein folding, J. Global Optimization, 15, 235-260 (1999).

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