Scheraga

Owicki J C and Scheraga H A 1977 Preferential sampling near solutes in Monte Carlo calculations on dilute solutions Chem. Phys. Lett. 47 600-2... 

Piela L, Kostrowicki J and Scheraga H A 1989 The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method J. Phys. Chem. 93 3339... 

Theory of helix-coil transitions in biopolymers. (Poland, D., Scheraga, H.A., eds) Academic Press, New York (1970)... 

Steinberg, I. Z., Scheraga, H. A. Entropy changes accompanying association reactions of proteins. J. Biol. Chem. 238 (1963)172-181. 

J. Kostrowicki and H.A. Scheraga, Application of the diffusion equation method for global optimization to oligopeptides, J. Phys. Chem. 96 (1992), 7442-7449. M. Levitt, A simplified representation of protein confomations for rapid simulation of protein folding, J. Mol. Biol. 104 (1976), 59-107. 

M. H. Hao, M. R. Pincus, S. Rackovsky, and H. A. Scheraga. Unfolding and refolding of the native structure of bovine pancreatic trypsin inhibitor studied by computer simulations. Biochemistry, 32 9614-9631, 1993. 

D.R. Ripoll, H.A. Scheraga, ECEPP Empirical Conformational Energy Program for Peptides, in The Encyclopedia of Computational Chemistry, Vol. 2,... 

Gibson K D and H A Scheraga 1987. Revised Algorithms for the Build-up Procedure for Predicting lAotein Conformations by Energy Minimization, journal of Computational Chemistry 8 826-834. 

Q and H A Scheraga 1987. Monte-Carlo-minimization Approach to the Multiple-minima Problem... 

Go N and H A Scheraga 1970. Ring Qosure and Local Cnnformational Deformations of C Molaarles. Macromolecules 3 178-187. 

Li Z Q and H A Scheraga 1987. Monte Carlo Minimization Approach to the Multiple Minima Problem, in Protein Folding. Proceedings of the National Academy of Sciences USA 84 6611-6615. 

RipoU D R and H A Scheraga 1988. On the Multiple-Mirumum Problem in the Conformational Anal of Polypeptides. II. An Electrostatistically Driven Monte Carlo Method Tests on Poly(L-Alani Biopolymers 27 1283-1303. 

A. R. Leach Molecular Modelling Principles and Applications Longman, Essex (1996). M. Vasquez, G. Nemethy, fJ. A. Scheraga, Cltem. Rev. 94, 2183 (1994). 

PROAIM PEOE Methods for Charges Gasteiger, Scheraga, Gombar (HDI)... 

G Nemethy, KD Gibson, KA Palmer, CN Yoon, G Paterlmi, A Zagari, S Rumsey, HA Scheraga. J Phys Chem 96 6472-6484, 1992. 

A Liwo, S Oldziej, MR Pmcus, RJ Wawak, S Rackovsky, HA Scheraga. J Comput Chem 18 849-876, 1997. 

KD Gibson, HA Scheraga. In RH Sarma, MH Sarma, eds. Structure and Expression, Vol 1, From Proteins to Ribosomes. New York Adenine Press, 1988, pp 67-94. 

Here,. Ai(X) is the partial SASA of atom i (which depends on the solute configuration X), and Yi is an atomic free energy per unit area associated with atom i. We refer to those models as full SASA. Because it is so simple, this approach is widely used in computations on biomolecules [96-98]. Variations of the solvent-exposed area models are the shell model of Scheraga [99,100], the excluded-volume model of Colonna-Cesari and Sander [101,102], and the Gaussian model of Lazaridis and Karplus [103]. Full SASA models have been used for investigating the thermal denaturation of proteins [103] and to examine protein-protein association [104]. 

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