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Inferring ideal amino acid interaction forms from statistical protein contact potentials |
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| Authors: | Pokarowski Piotr Kloczkowski Andrzej Jernigan Robert L Kothari Neha S Pokarowska Maria Kolinski Andrzej |
| Affiliation: | Institute of Applied Mathematics and Mechanics, Warsaw University, Warsaw, Poland. pokar@mimuw.ed.pl |
| Abstract: | We have analyzed 29 different published matrices of protein pairwise contact potentials (CPs) between amino acids derived from different sets of proteins, either crystallographic structures taken from the Protein Data Bank (PDB) or computer-generated decoys. Each of the CPs is similar to 1 of the 2 matrices derived in the work of Miyazawa and Jernigan (Proteins 1999;34:49-68). The CP matrices of the first class can be approximated with a correlation of order 0.9 by the formula e(ij) = h(i) + h(j), 1 |
| Keywords: | protein folding protein structure prediction threading residue‐based contact potentials statistical potentials knowledge‐based potentials |
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