1999/02/26 by Giovanni Settanni, Cristian Micheletti, Settanni, Giovanni +5
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #FOS: Biological sciences #FOS: Physical sciences #Quantitative Biology (q-bio) #Soft Condensed Matter (cond-mat.soft) #cond-mat.soft #q-bio
paper · pdf · doi:10.48550/arxiv.cond-mat/9902364
20 pages, 6 figures, submitted to J. Mol. Biol
arxiv created 1999/02/26 · arxiv updated 2009/11/30
An optimization technique is used to determine the pairwise interactions between amino acids in globular proteins. A numerical strategy is applied to a set of proteins for maximizing the native fold stability with respect to alternative structures obtained by gapless threading. The extracted parameters are shown to be very reliable for identifying the native states of proteins (unrelated to those in the training set) among thousands of conformations. The only poor performers are proteins with heme groups and/or poor compactness whose complexity cannot be captured by standard pairwise energy functionals.