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Biophys Physicobiol. 2017 Jul 12;14:99-110. doi: 10.2142/biophysico.14.0_99. eCollection 2017.

Monte Carlo simulation of a statistical mechanical model of multiple protein sequence alignment.

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Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.


A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are used for both parameter optimization of the model and production runs to explore the sequence subspace around a given protein family. In this Note, I describe the details of the MC algorithm as well as some preliminary results of MC simulations with various temperatures and chemical potentials, and compare them with the mean-field approximation. The existence of a two-state transition in the sequence space is suggested for the SH3 domain family, and inappropriateness of the mean-field approximation for the LGM is demonstrated.


Metropolis algorithm; mean-field approximation; protein folding; protein structure

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