Monte homology model

K. Ogata, M. Ohya, H. Umeyama. Amino acid similarity matrix for homology modeling derived from structural alignment and optimized by the Monte Carlo method. J Mol Graph Model. 1998, 16, 178-189, 254. 

Zimmer, R. and J. Halfmann, Optimizing Homology Models of protein structures with potentials of mean force, in Monte Carlo Approach to Biopolymers and protein Folding, P. B. Grassberger, G., Nadler, W., Editor. 1998, World Scientific, p. 45-68. 

This section explains basic principles of Monte-Carlo models, which are also successfully applied for the evaluation of adsorption enthalpies in gas-phase and vacuum adsorption chromatography investigations of the heaviest elements and their lighter homologs (see chapters Experimental Techniques and Gas-Phase... 

L. Holm, C. Sander. Fast and simple Monte Carlo algorithm for side chain optimization in proteins Application to model building by homology. Proteins. 1992, 14, 213-223. 

All models need some binary interaction parameters that have to be adjusted to some thermodynamic equihbriirm properties since these parameters are a priori not known (we will not discuss results from Monte Carlo simulations here). Binary parameters obtained from data of dilute polymer solutions as second virial coefficients are often different from those obtained from concentrated solutions. Distinguishing between intramolecular and intermolecular segment-segment interactions is not as important in concentrated solutions as it is in dilute solutions. Attempts to introduce local-composition and non-random-mix-ing approaches have been made for all the theories given above with more or less success. At least, they introduce additional parameters. More parameters may cause a higher flexibility of the model equations but leads often to physically senseless parameters that cause troubles when extrapolations may be necessary. Group-contribution concepts for binary interaction parameters in equation of state models can help to correlate parameter sets and also data of solutions within homologous series. 

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