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Polarizable protein packing
Author(s) -
Ng Albert H.,
Snow Christopher D.
Publication year - 2011
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21714
Subject(s) - polarizability , force field (fiction) , conformational isomerism , computer science , hypergraph , combinatorial optimization , mathematical optimization , mathematics , computational chemistry , chemistry , combinatorics , physics , artificial intelligence , quantum mechanics , molecule
To incorporate protein polarization effects within a protein combinatorial optimization framework, we decompose the polarizable force field AMOEBA into low order terms. Including terms up to the third‐order provides a fair approximation to the full energy while maintaining tractability. We represent the polarizable packing problem for protein G as a hypergraph and solve for optimal rotamers with the FASTER combinatorial optimization algorithm. These approximate energy models can be improved to high accuracy [root mean square deviation (rmsd) < 1 kJ mol −1 ] via ridge regression. The resulting trained approximations are used to efficiently identify new, low‐energy solutions. The approach is general and should allow combinatorial optimization of other many‐body problems. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011