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Cover Image, Volume 35, Issue 32
Publication year - 2014
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Reports
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23779
Subject(s) - flexibility (engineering) , cover (algebra) , computer science , volume (thermodynamics) , algorithm , cartesian coordinate system , dna , image (mathematics) , computer graphics (images) , theoretical computer science , information retrieval , data mining , artificial intelligence , physics , mathematics , biology , geometry , engineering , statistics , quantum mechanics , genetics , mechanical engineering
The flexibility of DNA is important for protein‐DNA binding and sequence recognition. To quantify this flexibility, Aleksandra Karolak and Arjan van der Vaart introduce on page 2297 (DOI: 10.1002/jcc.23751 ) a simplified method to calculate DNA step parameters and their Cartesian derivatives for use in molecular dynamics free energy simulations. Using three atoms per base and no structure overlays, the step parameters are calculated in a highly efficient manner while retaining good accuracy. The method is illustrated by calculating the flexibility of the central CG step in methylated and unmethylated DNA strands.