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Cover Image, Volume 37, Issue 29
Publication year - 2016
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.24510
Subject(s) - cover (algebra) , computer science , nucleosome , volume (thermodynamics) , algorithm , monte carlo method , image (mathematics) , energy (signal processing) , sampling (signal processing) , computer graphics (images) , data mining , information retrieval , artificial intelligence , dna , mathematics , computer vision , physics , chemistry , statistics , histone , mechanical engineering , engineering , biochemistry , filter (signal processing) , quantum mechanics
An illustration of the B‐DNA Monte Carlo algorithm is presented by Steven C. Howell, Xiangyun Qiu, and Joseph E. Curtis on page 2553 (DOI: 10.1002/jcc.24474 ). The algorithm uses a wormlike bead‐rod model for rapidly sampling B‐DNA configurations. All‐atom coordinates are used to build the bead‐rod model. After MC sampling of the bead‐rod model, atomic coordinates are recovered from the coarse‐grained configuration. Candidate structures are energy minimized to obtain robust models for comparing to experimental data. Examples demonstrate applying the method to a nucleosome and nucleosome array. An implementation of the algorithm with additional protein moves and energy minimization utilities are available at sassie-web.chem.utk.edu .