Computational Protein Folding

What Lessons Are To Be Learned from Computational Protein Folding Research ... 

WHAT LESSONS ARE TO BE LEARNED FROM COMPUTATIONAL PROTEIN FOLDING RESEARCH ... 

IBM (Blue Gene project) 2000 Computational protein folding www.ibm.com/ news/1999/12/06. phtml... 

The examples of modelling discussed in section C2.5.2 and section C2.5.3 are meant to illustrate tlie ideas behind tlie tlieoretical and computational approaches to protein folding. It should be borne in mind tliat we have discussed only a very limited aspect of tlie rich field of protein folding. The computations described in section C2.5.3 can be carried out easily on a desktop computer. Such an exercise is, perhaps, tlie best of way of appreciating tlie simple approach to get at tlie principles tliat govern tlie folding of proteins. 

Taketomi H, Ueda Y and Go N 1975 Studies on protein folding, unfolding, and fluctuations by computer simulation Int. J. Pept. Protein Res. 7 445-59... 

Wang J and Wang W 1999 A computational approach to simplifying the protein folding alphabet Natur. Struct. Biol. 6 1033-8... 

M. Levitt and A. Warshel, Computer simulation of protein folding. Nature 253 (1975), 694-698. 

G. Ramachandran and T. Schlick. Beyond optimization Simulating the dynamics of supercoiled DNA by a macroscopic model. In P. M. Pardalos, D. Shal-loway, and G. Xue, editors. Global Minimization of Nonconvex Energy Functions Molecular Conformation and Protein Folding, volume 23 of DIM ACS Series in Discrete Mathematics and Theoretical Computer Science, pages 215-231, Providence, Rhode Island, 1996. American Mathematical Society. 

RA Friesner, JR Gunn. Computational studies of protein folding. Annu Rev Biophys Biomol Struct 25 315-342, 1996. 

C Wilson, S Doniach. A computer model to dynamically simulate protein folding Studies with crambm. Proteins 6 193-209, 1989. 

Naturally, the pivotal role of protein folding in biophysics and biochemistry has yielded a very large body of research. In this chapter we focus primarily on the different theoretical and computational approaches that have contributed to the current understand-... 

The current understanding of the protein folding process has benefited much from studies that focus on computer simulations of simplified lattice models. These studies try to construct as simple a model as possible that will capture some of the more important properties of the real polypeptide chain. Once such a model is defined it can be explored and studied at a level of detail that is hard to achieve with more realistic (and thus more complex) atomistic models. 

H Taketomi, Y Ueda, N Go. Studies on protein folding, unfolding and fluctuations by computer simulation. 1. The effect of specific ammo acid sequence represented by specific mter-umt interactions. Int J Peptide Protein Res 7 445-459, 1975. 

In addition to being a remarkable demonstration of the power of computer-based combinatorial design of a protein fold, this designed peptide is the shortest known peptide consisting entirely of naturally occurring amino acids that folds into a well-ordered structure without metal binding, oligomerization or disulfide bond formation. 

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