TY - JOUR T1 - Coarse-grained simulations of membrane insertion and folding of small helical proteins using CABS model JF - Journal of Chemical Information and Modeling Y1 - 2016 A1 - Wojciech Pulawski A1 - Michal Jamroz A1 - Michal Kolinski A1 - Andrzej KoliƄski A1 - Sebastian Kmiecik AB - The CABS coarse-grained model is a well-established tool for modeling globular proteins (predicting their structure, dynamics and interactions). Here we introduce an extension of CABS representation and force field (CABS-membrane) to the modeling of the effect of biological membrane environment on the structure of membrane proteins. We validate the CABS-membrane model in folding simulations of 10 short helical membrane proteins not using any knowledge about their structure. The simulations start from random protein conformations placed outside the membrane environment and allow for full flexibility of the modeled proteins during their spontaneous insertion into the membrane. In the resulting trajectories, we have found models close to the experimental membrane structures. We also attempted to select the correctly folded models using simple filtering followed by structural clustering combined with reconstruction to all-atom representation and all-atom scoring. In conclusion, the CABS-membrane model is a promising approach for further development towards modeling of large protein-membrane systems. VL - 56 UR - https://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00350 IS - 11 ER -