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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

Version of Record online: 1 SEP 2012 | DOI: 10.1002/jcc.23099

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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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