Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 15, Issue 5, Pages 3306-3315Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.8b01133
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Funding
- National Institute of General Medical Sciences of the National Institute of Health [R01-GM063796]
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Standard low resolution coarse-grained modeling techniques have difficulty capturing multiple configurations of protein systems. Here, we present a method for creating accurate coarse-grained (CG) models with multiple configurations using a linear combination of functions or states. Individual CG models are created to capture the individual states, and the approximate coupling between the two states is determined from an all-atom potential of mean force. We show that the resulting multi configuration coarse-graining (MCCG) method accurately captures the transition state as well as the free energy between the two states. We have tested this method on the folding of dodecaalanine, as well as the amphipathic helix of endophilin.
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