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Distance‐dependent, pair potential for protein folding: Results from linear optimization
Author(s) -
Tobi Dror,
Elber Ron
Publication year - 2000
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/1097-0134(20001001)41:1<40::aid-prot70>3.0.co;2-u
Subject(s) - decoy , pairwise comparison , folding (dsp implementation) , function (biology) , potential energy , energy (signal processing) , interval (graph theory) , statistical potential , algorithm , mathematics , biological system , combinatorics , statistical physics , computer science , physics , statistics , chemistry , protein structure , biology , protein structure prediction , atomic physics , evolutionary biology , engineering , biochemistry , nuclear magnetic resonance , receptor , electrical engineering
The results of an optimization of a folding potential are reported. The complete energy function is modeled as a sum of pairwise interactions with a flexible functional form. The relevant distance between two amino acids (2 − 9 Å) is divided into 13 intervals, and the energy of each interval is optimized independently. We show, in accord with a previous publication (Tobi et al., Proteins 2000;40:71–85) that it is impossible to find a pair potential with the above flexible form that recognizes all native folds. Nevertheless, a potential that rates correctly a subset of the decoy structures was constructed and optimized. The resulting potential is compared with a distance‐dependent statistical potential of Bahar and Jernigan. It is further tested against decoy structures that were created in the Levitt's group. On average, the new potential places native shapes lower in energy and provides higher Z scores than other potentials. Proteins 2000;41:40–46. © 2000 Wiley‐Liss, Inc.