Abstract
Key problems in computational biology, including protein and RNA folding and drug docking, involve conformational searching over multidimensional potential surfaces with very large numbers of local minima. This paper shows how statistics provided by the CGU global optimization algorithm can be used to characterize and interpret these topographies using a 2-dimensional landscape projection.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Phillips, A.T., Rosen, J.B., & Walke, V.H. (1995), “Molecular structure determination by global optimization,” Dimacs Series in Discrete Mathematics and Theoretical Computer Science 23:181–198.
Dill, K.A. & Chan, H.S. (1997), “Prom Levinthal to pathways to funnels,” Nature Structural Biology 4(1):10–19.
Leopold, RE., Montal, M., & Onuchic, J.N. (1992), “Protein folding funnels: A kinetic approach to the sequence structure relationship,” Proc. Natl. Acad. Sci. USA 89:8721–8725.
Socci, N.D., & Onuchic, J.M. (1994), “Folding kinetics of protein-like heteropolymers,” J Chem Phys 100:1519–1528.
Wolynes, P.G., Onuchic, J.N., & Thirumalai, D. (1995), “Navigating the folding routes,” Science 267:1619–1620.
Bryngelson, J.D. & Wolynes, P.G. (1987), “Spin-glass and the statistical mechanics of protein folding,” Proc. Natl. Acad. Sci. USA 84:7524–7528.
Bryngelson, J.D. & Wolynes, P.G. (1989), “Intermediates and barrier crossing in a random energy model (with applications to protein folding),” J. Phys. Chem. 93:6902–6915.
Dill, K.A. (1987), “The stabilities of globular proteins,” In Protein Engineering (eds Oxender, D.L. & Fox, C.F.) 187–192 (Alan R. Liss, Inc., New York, 1987).
Phillips, A.T., Rosen, J.B. & Dill, K.A. (1999), “Convex global underestimation for molecular structure prediction,” in From Local to Global Optimization (eds P.M. Pardalos et al.) in press (Kluwer, Dordrecht, 1999).
Dill, K.A., Phillips, A.T. & Rosen, J.B. (1997), “Protein structure and energy landscape dependence on sequence using a continuous energy function,” Journal of Computational Biology 4(3):227–239.
Dill, K.A., Phillips, A.T. & Rosen, J.B. (1997), “Molecular structure prediction by global optimization,” in Developments in Global Optimization (eds I.M. Bomze et al.) 217–234 (Kluwer, Dordrecht, 1997).
Dill, K.A., Phillips, A.T. & Rosen, J.B. (1997), “CGU: An algorithm for molecular structure prediction,” in IMA Volumes in Mathematics and its Applications: Large-Scale Optimization with Applications III: Molecular Structure and Optimization (eds L.T. Biegler et al.) 1–22.
Sun, S., Thomas, P.D. & Dill, K.A. (1995), “A simple protein folding algorithm using binary code and secondary structure constraints,” Protein Engineering 8(8): 769–778.
Maiorov, V.N. & Crippen, G.M. (1994), “Learning about protein folding via potential functions,” Proteins Struct. Funct. Genet. 20:167–173.
Koretke, K.K., Luthey-Schulten, Z. & Wolynes, P.G. (1998), “Self-consistency optimized energy functions for protein structure prediction by molecular dynamics,” Proc. Natl. Acad. Sci. USA 95:2932–2937.
Hao, M.H. & Scheraga, H.A. (1996), “How optimization of potential functions affects protein folding,” Proc. Natl. Acad. Sci. USA 93:4984–4989.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2000 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Phillips, A.T., Ben Rosen, J., Dill, K.A. (2000). Energy Landscape Projections of Molecular Potential Functions. In: Floudas, C.A., Pardalos, P.M. (eds) Optimization in Computational Chemistry and Molecular Biology. Nonconvex Optimization and Its Applications, vol 40. Springer, Boston, MA. https://doi.org/10.1007/978-1-4757-3218-4_3
Download citation
DOI: https://doi.org/10.1007/978-1-4757-3218-4_3
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4419-4826-7
Online ISBN: 978-1-4757-3218-4
eBook Packages: Springer Book Archive