Susanne Pape, Franziska Hoffgaard, Mirjam Dür and Kay Hamacher Distance dependency and minimum amino acid alphabets for decoy scoring potentials Journal of Computational Chemistry 34
Protein structure is determined by amino acid interactions and thus sequence specific. The 3D-fold of a protein gives rise to distance-dependent interactions of the amino acids. In this article, the full distance dependency is derived by formulating the underlying modeling problem as a linear program. Upon solving this optimization problem for the full or reduced amino acid alphabets, one obtains new insight into structure threading and protein evolution.
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