Proteins conformation prediction

Fasman, G.D. Protein conformational prediction. Trends Biochem. Sci. 14 295-299, 1989. 

Fasman, G.D. (1990). Protein conformational prediction. In Proteins Form and Function. R.A.Bradshaw and M.Purton, eds. (Cambridge Elsevier Trends loumals), pp. 135 145. 

Steven M. Muskal s program for neural network simulator for protein conformation prediction and other data analysis. PCs under DOS. 

Dr. Steven M. Muskal s program for neural network simulator for protein conformation prediction and other data analysis. BLSS for statistics. Miscellaneous programs available by anonymous ftp from berkeley.edu in directory /pub. PCs (DOS), Macintosh, UNIX workstations. 

EE Cohen, ID Kuntz. Tertiary stiaicture prediction. In CD Easman, ed. Prediction of Protein Structure and the Principles of Protein Conformation. New York Plenum Press, 1989, pp 647-705. 

RJ Petrella, T Lazardis, M Karplus. Protein sidecham conformer prediction A test of the energy function. Folding Des 3 353-377, 1998. 

Baumgartner and coworkers [145,146] study lipid-protein interactions in lipid bilayers. The lipids are modeled as chains of hard spheres with heads tethered to two virtual surfaces, representing the two sides of the bilayer. Within this model, Baumgartner [145] has investigated the influence of membrane curvature on the conformations of a long embedded chain (a protein ). He predicts that the protein spontaneously localizes on the inner side of the membrane, due to the larger fluctuations of lipid density there. Sintes and Baumgartner [146] have calculated the lipid-mediated interactions between cylindrical inclusions ( proteins ). Apart from the... 

Fasman G (1989) Prediction of protein structure and the principles of protein conformation. Plenum Press, New York... 

J. S. Richardson D. C. Richardson, Principles and Patterns of Protein Conformation. In Prediction of Protein Structure and the Priciples of Protein Conformation G. D. Fasman, Ed. Plenum Press New York, 1989 pp 1-98. 

Summary. We recently developed an all-atom free energy force field (PFFOl) for protein structure prediction with stochastic optimization methods. We demonstrated that PFFOl correctly predicts the native conformation of several proteins as the global optimum of the free energy surface. Here we review recent folding studies, which permitted the reproducible all-atom folding of the 20 amino-acid trp-cage protein, the 40-amino acid three-helix HIV accessory protein and the sixty amino acid bacterial ribosomal protein L20 with a variety of stochastic optimization methods. These results demonstrate that all-atom protein folding can be achieved with present day computational resources for proteins of moderate size. 

This review indicates that all-atom protein structure prediction with stochastic optimization methods becomes feasible with present-day computational resources. The fact that three proteins were reproducibly folded with different optimization methods to near-native conformation increases the confidence in the parameterization of our all-atom protein force field PFFOl. The... 

Chou, P.Y. and Fasman, G.D. (1974b) Prediction of Protein Conformation. 

Gamier, J. and Robson, B. (1989) The GOR Method for predicting Secondary Stmctures in Proteins. In Prediction of Protein Structure and the Principles ofProtein Conformation, edited by G.D.Fasman. New York Plenum Press. 

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