Computational Protein Design by Ilan Samish

Author:Ilan Samish
Language: eng
Format: epub
Publisher: Springer New York, New York, NY

(3)

As in ref. 8, the SASA res is transformed into a solvent accessibility index (SAI) based on the relative rank among all positions in the training data set. Geometry of the pseudo sidechain and the weights in Eq. (3) have been optimized so that the resulting SAI for a position contains maximally residue-type information in the training data set.

3.As in ref. 8, van der Waals energies may be combined, with weights, with the SEF. The weights of the van der Waals terms depend solely on the solvent accessibility of the positions involved. Instead of categorizing the positions into three discrete categories and use one van der Waals weight for each category, in the current program the following continuous function is employed to determine the van der Waals weight based on SAI:

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