Prediction of Oligopeptide Conformations via Deterministic Global Optimization

Journal of Global Optimization

Volumn 11, Issue 1, 1997, Pages 1-34

  Androulakis, I P ^a   Maranas, C D ^b   Floudas, C A ^c  

^a EXXONMOBIL UPSTREAM RESEARCH COMPANY   (United States)

^b The Pennsylvania State University   (United States)

^c Princeton University   (United States)

Author keywords

Deterministic global optimization; Protein folding

Indexed keywords

EID: 1842639266     PISSN: 09255001     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1008224308626     Document Type: Article

References (48)

1. C. Adjiman, I.P. Androulakis, C.D Maranas, and C.A. Floudas, A Global Optimization Method, αBB, for Process Design. Comp. and Chem. Eng., 20:S419-S424, 1966.
2. C. Adjiman and C.A. Floudas, Rigorous Convex Underestimators for General Twice-Differentiable Problems. J. Global Opt., 9:23-40, 1996.
3. 2 Tortional Terms. J. Am. Chem. Soc., 99:8127-8134, 1977.
4. N.L. Allinger, Y.H. Yuh, and J.-H. Lii, Molecular Mechanics. The MM3 Force Field for Hydrocarbons. J. Am. Chem. Soc., 111:8551-8582, 1989.
5. I.P. Androulakis, C.D. Maranas and C.A. Floudas, αBB: A Global Optimization Method for General Constrained Nonconvex Problems. J. Global Opt., 7:337-363, 1995.
6. I.P. Androulakis, C.D. Maranas, and C.A. Floudas, αBB: A Global Optimization Method for General Constrained Nonconvex Problems. Paper presented at the AIChE Annual Meeting, Miami, FL, 1995.
7. I.P. Androulakis, C.D. Maranas, and C.A. Floudas, Distributed Branch and Bound Algorithms for Global Optimization. Paper presented at the AIChE Annual Meeting, Miami, FL, 1995.
8. C.B. Anfinsen, E. Haber, M. Sela, and F.H. White, The Kinetics of Formation of Native Ribonuclease During Oxidation of the Reduced Polypeptide Chain. J. Proc. Nat. Acad. Sci. U.S.A., 47:1309-1314, 1961.
9. F.C. Bernstein, T.F. Koetzle, G.J.B. Williams, E.F. Meyer Jr, M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi, he Protein Data Bank: A Computer-Based Archival File for Macromolecular Structures. J. Mol. Biol., 12:535-542, 1977.
10. B. Brooks, R. Bruccoleri, B. Olafson, D. States, S. Swaminathan, and M. Karplus, CHARM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comp., Chem., 4:187-217, 1983.
11. T.E. Creighton, Proteins: Structures and Molecular Properties, W.H. Freeman and Company, New York, 1993.
12. P. Dauber-Osguthorpe, V.A. Roberts, D.J. Osguthorpe, J. Wolff, M. Genest and A.T. Hagler, Structure and Energetics of Ligand Bindings to Peptides: Escherichia coli Dihydrofolate Reductase-Trimethoprim, A Drug Receptor System. Proteins: Struct. Funct. Genet., 4:31-47, 1988.
13. B. Freyberg and W.J. Braun, Efficient Search for All Low Energy Conformations of Polypeptides by Monte Carlo Methods. J. Comp. Chem., 12:1065-1076, 1991.
14. L. Glasser and H.A. Scheraga, Calculations on Crystall Packing of a Flexible Molecule, Leu-Enkephalin. J. Mol. Biol., 199:513-524, 1988.
15. U.H. Hansmann and Y. Okamoto, Prediction of Peptide Conformation my Multicanonical Algorithm: New Approach to the Multiple-Minima Problem. J. Comp. Chem., 14:1333-1338, 1993.
16. A.J. Hopfinger, Conformational Properties of Macromolecules. Academic Press, New York, NY, 1973.
17. J. Kostrowicki and H.A. Scheraga, Application of the Diffusion Equation Method for Global Optimization to Oligopeptides. J. Phys. Chem., 96:7442-7449, 1992.
18. M.H. Lambert and H.A. Scheraga, Payttern Recognition in the Prediction of Protein Structure I. Tripeptide Conformational Probabilities Calculated from the Amino Acid Sequence. J. Comp. Chem., 6:770-797, 1989.
19. M. Levitt, Protein Folding by Restrained Energy Minimization and Molecular Dynamics. J. Mol. Biol., 170:723-764, 1983.
20. Z. Li and H.A. Scheraga, Structure and Free Energy of Complex Thermodynamic Systems. J. Mol. Struct. (Theochem.), 179:333-352, 1988.
21. C.D. Maranas and C.A. Floudas, A Global Optimization Approach for Lennard-Jones Microclusters. J. Chem. Phys., 97:7667-7678, 1992.
22. C.D. Maranas and C. A. Floudas, Global Optimization for Molecular Conformation Problems. Ann. Oper. Res., 42:85-117, 1993.
23. C.D. Maranas and C.A. Floudas, Global Minimum Potential Energy Conformations of Small Molecules. J. Global Opt., 4:135-170, 1994.
24. C.D. Maranas and C.A. Floudas, A Deterministic Global Optimization Approach for Molecular Structure Determination. J. Chem. Phys., 100:1247-1261, 1994.
25. C.D. Maranas, I.P. Androulakis, and C.A. Floudas, A Deterministic Global Optimization Approach for the Protein Folding Problem, Global Optimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding. P.M. Pardalos, D. Shaloway, and G. Xue (Eds.). DIMACS Series in Discrete Mathematics and Theoretical Computer Science, American Mathematical Society, 23:133-150, 1996.
26. B.A. Murtagh and M.A. Saunders, MINOS5.0 Users Guide. Systems Optimization Laboratory, Dept. of Operations Research, Stanford University, CA., 1983.
27. F.A. Momany, L.M. Carruthers, R.F. McGuire, and H.A. Scheraga, Intermolecular Potentials from Crystal Data. III,. Determination of Empirical Potentials and Applications to the Packing Configurations and Lattice Energies in Crystals of Hydrocarbons, Carboxylic Acids, and Amides. J. Phys. Chem., 78:1595-1620, 1974.
28. F.A. Momany, L.M. Carruthers, and H.A. Scheraga, Intermolecular Potentials from Crystal Structures. III. Application of Empirical Potentials to the Packing Configurations and Lattice Energies in Crystals of Ainino Acids. J. Phys. Chem., 78:1621-1630, 1974.
29. F.A. Momany, R.F. McGuire, A.W. Burgess, and H.A. Scheraga, Energy Parameters in Polypeptiudes. VII Geometric Parameters, Patial Atomic Charges, Nonbonded Interactions, Hydrogen Bond Interactions, and Intrinsic Torsional Potentials for the Naturally Occuring Amino Acids. J. Phys. Chem., 79:2361-2381, 1975.
30. L.B. Moralles, R. Garduno-Juarez, and D. Romero, Applications of Simulated Annealling to the Multiple-Minima Problem in Small Peptides. J. Biomol. Struct. Dynamics, 8:721-735, 1991.
31. L.B. Moralles, R. Garduno-Juarez, and D. Romero, The Multiple-Minima Porblem in Small Peptides Revisited. The Threshold Accepting Approach. J. Biomol. Struct. Dynamics, 9:951-957, 1992.
32. A. Nayeem, J. Vila, and H.A. Scheraga, A Comparative Study of the Simulated-Annealilng and Monte Carlo-with-Minimization Approaches to the Minimum-Energy Structures of Polypetides: Met-Enkephalin. J. Comp. Chem., 12:594-605, 1991.
33. G. Némethy, M.S. Pottle, and H.A. Scheraga, Energy Parameters in Polypeptides. 9. Updating of Geometrical Parameters, Nonbonbed Interaction, and Hydrogen Bond Interactions for the Naturally Occuring Amino Acids. J. Phys. Chem., 89:1883-1887, 1983.
34. G. Némethy, K.D. Gibson, K.A. Palmer, C.N. Yoon, G. Paterlini, A. Zagari, S. Rumsey, and H.A. Scheraga, Energy Parameters in Polypeptides, 10. Improved Geometrical Parameters and Nonbonded Interactions for Use in the BCEPP/3 Algorithms, with Applications to Proline-Containing Peptides. J. Phys. Chem., 96;6472-6484, 1992.
35. A. Neumaier, Molecular Modeling of Proteins: The Mathematical Prediction of Protein Structure. SIAM Review, submitted for publication, 1995.
36. K.A. Olszewiski, L. Piela, and H.A. Scheraga, Mean Field Theory as a Tool for Intramolecular Coformational Optimization. Tests on Terminally-Blocked Alanine and Met enkeplhalin. J. Phys. Chem., 96:4672-4676, 1992.
37. P.M. Pardalos, D. Shalloway, and G. Xue (Eds.), Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, DIMACS series in Discrete Mathematics and Theoretical Computer Science, 23, Providence, RI, American Mathematical Society, 1996.
38. D.R. Ripoll and H.A. Scheraga, On the Multiple-Minima Problem in the Conformational Analysis of Polypeptides. II An Electrostatically Driven Monte Carlo Method - Tests of Poly(L-Alanine). Biopolymers, 27:1283-1303, 1988.
39. D.R. Ripoll and H.A. Scheraga, The Multiple Minima Problem in the Conformational Analysis of Polypeptides. III. An Electrostatically Driven Monte Carlo Method - Tests on Enkephalin. J. Protein Chem., 8:263-287, 1989.
40. D.R. Ripoll, M. Vásquez, and H.A. Scheraga, The Electrostatically Driven Monte Carlo Method; Application to conformational Analysis of Decaglycine. Biopolymers, 31:319-330, 1991.
41. H.A. Scheraga, Reviews in Computational Chemistry. VCH Publishers, New York, NY, 1992.
42. J. Shin and M. Jhon, High Directional Monte Carlo Procedure Coupled with the Temperature and Annealing Method to Obtain the Global Energy Minimum Structure of Polypeptides and Proteins. Biopolymers, 31:177-185, 1991.
43. B.L. Sibanda and J.M. Thorton, β-Hairpin families in globular proteins. Nature, 316:170-174, 1985.
44. W.F. van Gunsteren and H.J.C. Berendsen, GROMOS. Groningen Molecular Simulation, Groningen, The Netherlands, 1987.
45. M. Vásquez and H.A. Scheraga, Use of Buildup and Energy-Minimization Procedures to Compute Low-Energy Structures of the Backbone of Enkephalin. Macromolecules, 16:1043-1049, 1983.
46. M. Vásquez, G. Némethy, and H.A. Scheraga, Conformation Energy Calculations on Polypeptides and Proteina. Chem. Rev., 94;2183:2239, 1994.
47. S. Weiner, P. Kollmann, D.A. Case, U.C. Singh., C. Ghio, G. Alagona, S. Profeta and P. Weiner, A New Force Field for Molecular mechanical Simulation of Nucleic Acids and Proteins. J. Am. Chem. Soc., 106:765-784, 1984.
48. S. Weiner, P. Kollmann, D. Nguyen, and D. Case, An All Atom Force Field for Simulations of Proteins and Nucleic Acids. J. Comp. Chem., 7:230-252, 1986.