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From coarse‐grain to all‐atom: Toward multiscale analysis of protein landscapes
Author(s) -
Heath Allison P.,
Kavraki Lydia E.,
Clementi Cecilia
Publication year - 2007
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/prot.21371
Subject(s) - atom (system on chip) , energy landscape , folding (dsp implementation) , molecular dynamics , distortion (music) , statistical physics , biological system , protein folding , energy (signal processing) , computer science , algorithm , materials science , chemical physics , crystallography , physics , chemistry , computational chemistry , biology , thermodynamics , quantum mechanics , engineering , amplifier , computer network , bandwidth (computing) , nuclear magnetic resonance , electrical engineering , embedded system
Multiscale methods are becoming increasingly promising as a way to characterize the dynamics of large protein systems on biologically relevant time‐scales. The underlying assumption in multiscale simulations is that it is possible to move reliably between different resolutions. We present a method that efficiently generates realistic all‐atom protein structures starting from the C α atom positions, as obtained for instance from extensive coarse‐grain simulations. The method, a reconstruction algorithm for coarse‐grain structures (RACOGS), is validated by reconstructing ensembles of coarse‐grain structures obtained during folding simulations of the proteins src‐SH3 and S6. The results show that RACOGS consistently produces low energy, all‐atom structures. A comparison of the free energy landscapes calculated using the coarse‐grain structures versus the all‐atom structures shows good correspondence and little distortion in the protein folding landscape. Proteins 2007. © 2007 Wiley‐Liss, Inc.